Name: rs2308000
Published: September 21, 2022
License: Open Access

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

Reference SNP (rs) Report

This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs2308000

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr5:7871151-7871153 (GRCh38.p14) Help
The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.
Alleles: delCTT
Variation Type: Deletion
Frequency: CTT=0.416922 (110355/264690, TOPMED)
CTT=0.431015 (60212/139698, GnomAD)
delCTT=0.37069 (10475/28258, 14KJPN) (+ 13 more)
CTT=0.46690 (8647/18520, ALFA)
delCTT=0.37106 (6219/16760, 8.3KJPN)
CTT=0.4460 (2856/6404, 1000G_30x)
CTT=0.4571 (2289/5008, 1000G)
delCTT=0.4719 (2114/4480, Estonian)
delCTT=0.4881 (1881/3854, ALSPAC)
delCTT=0.4930 (1828/3708, TWINSUK)
delCTT=0.3952 (724/1832, Korea1K)
delCTT=0.498 (497/998, GoNL)
delCTT=0.473 (284/600, NorthernSweden)
delCTT=0.387 (82/212, Vietnamese)
CTT=0.50 (20/40, GENOME_DK)
delCTT=0.50 (20/40, GENOME_DK)

Clinical Significance: Reported in ClinVar
Gene : Consequence: MTRR : Intron Variant
Publications: 0 citations
Genomic View: See rs on genome

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	Alt HMOZ	HTRZ	HWEP
Total	Global	18520	CTT=0.46690	=0.53310	0.22851	0.294708	0.476782	9
European	Sub	14152	CTT=0.51208	=0.48792	0.264274	0.240107	0.495619	0
African	Sub	2898	CTT=0.2540	=0.7460	0.065562	0.557626	0.376812	0
African Others	Sub	114	CTT=0.228	=0.772	0.105263	0.649123	0.245614	3
African American	Sub	2784	CTT=0.2550	=0.7450	0.063937	0.553879	0.382184	0
Asian	Sub	112	CTT=0.607	=0.393	0.303571	0.089286	0.607143	3
East Asian	Sub	86	CTT=0.58	=0.42	0.255814	0.093023	0.651163	3
Other Asian	Sub	26	CTT=0.69	=0.31	0.461538	0.076923	0.461538	0
Latin American 1	Sub	146	CTT=0.445	=0.555	0.219178	0.328767	0.452055	0
Latin American 2	Sub	610	CTT=0.362	=0.638	0.12459	0.4	0.47541	0
South Asian	Sub	98	CTT=0.66	=0.34	0.367347	0.040816	0.591837	3
Other	Sub	504	CTT=0.486	=0.514	0.246032	0.27381	0.480159	0

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	CTT=0.416922	delCTT=0.583078
gnomAD - Genomes	Global	Study-wide	139698	CTT=0.431015	delCTT=0.568985
gnomAD - Genomes	European	Sub	75670	CTT=0.52105	delCTT=0.47895
gnomAD - Genomes	African	Sub	41822	CTT=0.26486	delCTT=0.73514
gnomAD - Genomes	American	Sub	13632	CTT=0.40684	delCTT=0.59316
gnomAD - Genomes	Ashkenazi Jewish	Sub	3316	CTT=0.4388	delCTT=0.5612
gnomAD - Genomes	East Asian	Sub	3112	CTT=0.5598	delCTT=0.4402
gnomAD - Genomes	Other	Sub	2146	CTT=0.4492	delCTT=0.5508
14KJPN	JAPANESE	Study-wide	28258	CTT=0.62931	delCTT=0.37069
Allele Frequency Aggregator	Total	Global	18520	CTT=0.46690	delCTT=0.53310
Allele Frequency Aggregator	European	Sub	14152	CTT=0.51208	delCTT=0.48792
Allele Frequency Aggregator	African	Sub	2898	CTT=0.2540	delCTT=0.7460
Allele Frequency Aggregator	Latin American 2	Sub	610	CTT=0.362	delCTT=0.638
Allele Frequency Aggregator	Other	Sub	504	CTT=0.486	delCTT=0.514
Allele Frequency Aggregator	Latin American 1	Sub	146	CTT=0.445	delCTT=0.555
Allele Frequency Aggregator	Asian	Sub	112	CTT=0.607	delCTT=0.393
Allele Frequency Aggregator	South Asian	Sub	98	CTT=0.66	delCTT=0.34
8.3KJPN	JAPANESE	Study-wide	16760	CTT=0.62894	delCTT=0.37106
1000Genomes_30x	Global	Study-wide	6404	CTT=0.4460	delCTT=0.5540
1000Genomes_30x	African	Sub	1786	CTT=0.2027	delCTT=0.7973
1000Genomes_30x	Europe	Sub	1266	CTT=0.5158	delCTT=0.4842
1000Genomes_30x	South Asian	Sub	1202	CTT=0.6539	delCTT=0.3461
1000Genomes_30x	East Asian	Sub	1170	CTT=0.5949	delCTT=0.4051
1000Genomes_30x	American	Sub	980	CTT=0.366	delCTT=0.634
1000Genomes	Global	Study-wide	5008	CTT=0.4571	delCTT=0.5429
1000Genomes	African	Sub	1322	CTT=0.2042	delCTT=0.7958
1000Genomes	East Asian	Sub	1008	CTT=0.5903	delCTT=0.4097
1000Genomes	Europe	Sub	1006	CTT=0.5249	delCTT=0.4751
1000Genomes	South Asian	Sub	978	CTT=0.655	delCTT=0.345
1000Genomes	American	Sub	694	CTT=0.367	delCTT=0.633
Genetic variation in the Estonian population	Estonian	Study-wide	4480	CTT=0.5281	delCTT=0.4719
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	CTT=0.5119	delCTT=0.4881
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	CTT=0.5070	delCTT=0.4930
Korean Genome Project	KOREAN	Study-wide	1832	CTT=0.6048	delCTT=0.3952
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	CTT=0.502	delCTT=0.498
Northern Sweden	ACPOP	Study-wide	600	CTT=0.527	delCTT=0.473
A Vietnamese Genetic Variation Database	Global	Study-wide	212	CTT=0.613	delCTT=0.387
The Danish reference pan genome	Danish	Study-wide	40	CTT=0.50	delCTT=0.50

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements

Sequence name	Change
GRCh38.p14 chr 5	NC_000005.10:g.7871151_7871153del
GRCh37.p13 chr 5	NC_000005.9:g.7871264_7871266del
MTRR RefSeqGene	NG_008856.1:g.7048_7050del
FASTKD3 RefSeqGene	NG_033101.1:g.2885_2887del

Gene: MTRR, 5-methyltetrahydrofolate-homocysteine methyltransferase reductase (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
MTRR transcript variant 6	NM_001364440.2:c.129+228_… NM_001364440.2:c.129+228_129+230del	N/A	Intron Variant
MTRR transcript variant 7	NM_001364441.2:c.129+228_… NM_001364441.2:c.129+228_129+230del	N/A	Intron Variant
MTRR transcript variant 8	NM_001364442.2:c.129+228_… NM_001364442.2:c.129+228_129+230del	N/A	Intron Variant
MTRR transcript variant 1	NM_002454.3:c.129+228_129… NM_002454.3:c.129+228_129+230del	N/A	Intron Variant
MTRR transcript variant 2	NM_024010.4:c.129+228_129… NM_024010.4:c.129+228_129+230del	N/A	Intron Variant
MTRR transcript variant 3	NR_134480.2:n.	N/A	Intron Variant
MTRR transcript variant 4	NR_134481.2:n.	N/A	Intron Variant
MTRR transcript variant 5	NR_134482.2:n.	N/A	Intron Variant
MTRR transcript variant 9	NR_157168.2:n.	N/A	Intron Variant
MTRR transcript variant 10	NR_157169.2:n.	N/A	Intron Variant
MTRR transcript variant 11	NR_157170.2:n.	N/A	Intron Variant
MTRR transcript variant 12	NR_157171.2:n.	N/A	Intron Variant
MTRR transcript variant 13	NR_157172.2:n.	N/A	Intron Variant
MTRR transcript variant 14	NR_157173.2:n.	N/A	Intron Variant
MTRR transcript variant 15	NR_157174.2:n.	N/A	Intron Variant
MTRR transcript variant 16	NR_157175.2:n.	N/A	Intron Variant
MTRR transcript variant 17	NR_157176.2:n.	N/A	Intron Variant
MTRR transcript variant 18	NR_157177.2:n.	N/A	Intron Variant
MTRR transcript variant 19	NR_157178.2:n.	N/A	Intron Variant
MTRR transcript variant X1	XM_024446064.2:c.129+228_… XM_024446064.2:c.129+228_129+230del	N/A	Intron Variant
MTRR transcript variant X2	XM_047417233.1:c.129+228_… XM_047417233.1:c.129+228_129+230del	N/A	Intron Variant
MTRR transcript variant X3	XM_047417234.1:c.129+228_… XM_047417234.1:c.129+228_129+230del	N/A	Intron Variant
MTRR transcript variant X4	XM_047417235.1:c.129+228_… XM_047417235.1:c.129+228_129+230del	N/A	Intron Variant
MTRR transcript variant X5	XM_047417236.1:c.129+228_… XM_047417236.1:c.129+228_129+230del	N/A	Intron Variant
MTRR transcript variant X6	XM_047417237.1:c.129+228_… XM_047417237.1:c.129+228_129+230del	N/A	Intron Variant
MTRR transcript variant X7	XM_047417238.1:c.129+228_… XM_047417238.1:c.129+228_129+230del	N/A	Intron Variant

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Allele: delCTT (allele ID: 1272031 )

ClinVar Accession	Disease Names	Clinical Significance
RCV001696316.1	not provided	Benign

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement	CTT=	delCTT
GRCh38.p14 chr 5	NC_000005.10:g.7871151_7871153=	NC_000005.10:g.7871151_7871153del
GRCh37.p13 chr 5	NC_000005.9:g.7871264_7871266=	NC_000005.9:g.7871264_7871266del
MTRR RefSeqGene	NG_008856.1:g.7048_7050=	NG_008856.1:g.7048_7050del
FASTKD3 RefSeqGene	NG_033101.1:g.2885_2887=	NG_033101.1:g.2885_2887del
MTRR transcript variant 6	NM_001364440.2:c.129+228=	NM_001364440.2:c.129+228_129+230del
MTRR transcript variant 7	NM_001364441.2:c.129+228=	NM_001364441.2:c.129+228_129+230del
MTRR transcript variant 8	NM_001364442.2:c.129+228=	NM_001364442.2:c.129+228_129+230del
MTRR transcript variant 1	NM_002454.2:c.129+228=	NM_002454.2:c.129+228_129+230del
MTRR transcript variant 1	NM_002454.3:c.129+228=	NM_002454.3:c.129+228_129+230del
MTRR transcript variant 2	NM_024010.2:c.210+228=	NM_024010.2:c.210+228_210+230del
MTRR transcript variant 2	NM_024010.4:c.129+228=	NM_024010.4:c.129+228_129+230del
MTRR transcript variant X1	XM_005248304.1:c.174+228=	XM_005248304.1:c.174+228_174+230del
MTRR transcript variant X2	XM_005248305.1:c.129+228=	XM_005248305.1:c.129+228_129+230del
MTRR transcript variant X1	XM_024446064.2:c.129+228=	XM_024446064.2:c.129+228_129+230del
MTRR transcript variant X2	XM_047417233.1:c.129+228=	XM_047417233.1:c.129+228_129+230del
MTRR transcript variant X3	XM_047417234.1:c.129+228=	XM_047417234.1:c.129+228_129+230del
MTRR transcript variant X4	XM_047417235.1:c.129+228=	XM_047417235.1:c.129+228_129+230del
MTRR transcript variant X5	XM_047417236.1:c.129+228=	XM_047417236.1:c.129+228_129+230del
MTRR transcript variant X6	XM_047417237.1:c.129+228=	XM_047417237.1:c.129+228_129+230del
MTRR transcript variant X7	XM_047417238.1:c.129+228=	XM_047417238.1:c.129+228_129+230del

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

61 SubSNP, 15 Frequency, 1 ClinVar submissions

No	Submitter	Submission ID	Date (Build)
1	MARSHFIELD	ss3255851	Sep 28, 2001 (100)
2	YUSUKE	ss4475390	Jul 03, 2002 (106)
3	ABI	ss42512374	Mar 14, 2006 (126)
4	HUMANGENOME_JCVI	ss95385375	Feb 06, 2009 (130)
5	BCMHGSC_JDW	ss103705059	Dec 01, 2009 (131)
6	GMI	ss154944944	Dec 01, 2009 (131)
7	BUSHMAN	ss193785756	Jul 04, 2010 (132)
8	BL	ss256039773	May 09, 2011 (135)
9	GMI	ss287766898	May 09, 2011 (134)
10	GMI	ss288611599	May 04, 2012 (137)
11	PJP	ss295211425	May 09, 2011 (135)
12	1000GENOMES	ss326633826	May 09, 2011 (135)
13	1000GENOMES	ss326672127	May 09, 2011 (135)
14	1000GENOMES	ss326870084	May 09, 2011 (135)
15	1000GENOMES	ss499021210	May 04, 2012 (137)
16	LUNTER	ss551469081	Apr 25, 2013 (138)
17	LUNTER	ss551612699	Apr 25, 2013 (138)
18	LUNTER	ss553184854	Apr 25, 2013 (138)
19	TISHKOFF	ss554162514	Apr 25, 2013 (138)
20	SSMP	ss663622796	Apr 01, 2015 (144)
21	BILGI_BIOE	ss666298471	Apr 25, 2013 (138)
22	EVA-GONL	ss981223980	Aug 21, 2014 (142)
23	1000GENOMES	ss1373401120	Aug 21, 2014 (142)
24	EVA_GENOME_DK	ss1576453599	Apr 01, 2015 (144)
25	EVA_DECODE	ss1590739732	Apr 01, 2015 (144)
26	EVA_UK10K_ALSPAC	ss1704552517	Apr 01, 2015 (144)
27	EVA_UK10K_TWINSUK	ss1704552572	Apr 01, 2015 (144)
28	HAMMER_LAB	ss1803022825	Sep 08, 2015 (146)
29	GENOMED	ss1970006588	Jul 19, 2016 (147)
30	JJLAB	ss2030663812	Sep 14, 2016 (149)
31	SYSTEMSBIOZJU	ss2625918064	Nov 08, 2017 (151)
32	GNOMAD	ss2820907106	Nov 08, 2017 (151)
33	SWEGEN	ss2996402588	Nov 08, 2017 (151)
34	MCHAISSO	ss3066002002	Nov 08, 2017 (151)
35	BEROUKHIMLAB	ss3644177995	Oct 12, 2018 (152)
36	BIOINF_KMB_FNS_UNIBA	ss3645858775	Oct 12, 2018 (152)
37	URBANLAB	ss3647980129	Oct 12, 2018 (152)
38	EGCUT_WGS	ss3664292071	Jul 13, 2019 (153)
39	EVA_DECODE	ss3714061346	Jul 13, 2019 (153)
40	ACPOP	ss3732068498	Jul 13, 2019 (153)
41	PACBIO	ss3785016870	Jul 13, 2019 (153)
42	PACBIO	ss3790435782	Jul 13, 2019 (153)
43	PACBIO	ss3795312317	Jul 13, 2019 (153)
44	KHV_HUMAN_GENOMES	ss3806205539	Jul 13, 2019 (153)
45	EVA	ss3829082457	Apr 26, 2020 (154)
46	EVA	ss3838003177	Apr 26, 2020 (154)
47	EVA	ss3843442783	Apr 26, 2020 (154)
48	KOGIC	ss3956055543	Apr 26, 2020 (154)
49	TOPMED	ss4648864999	Apr 26, 2021 (155)
50	TOMMO_GENOMICS	ss5170284196	Apr 26, 2021 (155)
51	1000G_HIGH_COVERAGE	ss5262800207	Oct 13, 2022 (156)
52	HUGCELL_USP	ss5461153229	Oct 13, 2022 (156)
53	1000G_HIGH_COVERAGE	ss5545810133	Oct 13, 2022 (156)
54	SANFORD_IMAGENETICS	ss5637139163	Oct 13, 2022 (156)
55	TOMMO_GENOMICS	ss5705931091	Oct 13, 2022 (156)
56	YY_MCH	ss5806001352	Oct 13, 2022 (156)
57	EVA	ss5834488334	Oct 13, 2022 (156)
58	EVA	ss5854671742	Oct 13, 2022 (156)
59	EVA	ss5892902897	Oct 13, 2022 (156)
60	EVA	ss5965549015	Oct 13, 2022 (156)
61	EVA	ss5980278316	Oct 13, 2022 (156)
62	1000Genomes	NC_000005.9 - 7871264	Oct 12, 2018 (152)
63	1000Genomes_30x	NC_000005.10 - 7871151	Oct 13, 2022 (156)
64	The Avon Longitudinal Study of Parents and Children	NC_000005.9 - 7871264	Oct 12, 2018 (152)
65	Genetic variation in the Estonian population	NC_000005.9 - 7871264	Oct 12, 2018 (152)
66	The Danish reference pan genome	NC_000005.9 - 7871264	Apr 26, 2020 (154)
67	gnomAD - Genomes	NC_000005.10 - 7871151	Apr 26, 2021 (155)
68	Genome of the Netherlands Release 5	NC_000005.9 - 7871264	Apr 26, 2020 (154)
69	Korean Genome Project	NC_000005.10 - 7871151	Apr 26, 2020 (154)
70	Northern Sweden	NC_000005.9 - 7871264	Jul 13, 2019 (153)
71	8.3KJPN	NC_000005.9 - 7871264	Apr 26, 2021 (155)
72	14KJPN	NC_000005.10 - 7871151	Oct 13, 2022 (156)
73	TopMed	NC_000005.10 - 7871151	Apr 26, 2021 (155)
74	UK 10K study - Twins	NC_000005.9 - 7871264	Oct 12, 2018 (152)
75	A Vietnamese Genetic Variation Database	NC_000005.9 - 7871264	Jul 13, 2019 (153)
76	ALFA	NC_000005.10 - 7871151	Apr 26, 2021 (155)
77	ClinVar	RCV001696316.1	Oct 13, 2022 (156)

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Associated ID	History Updated (Build)
rs10540907	Sep 24, 2004 (123)
rs35290562	May 23, 2006 (127)
rs139287124	Sep 17, 2011 (135)
rs139466081	Sep 17, 2011 (135)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss256039773, ss288611599, ss295211425, ss326633826, ss326672127, ss326870084, ss551469081, ss551612699, ss553184854, ss1590739732	NC_000005.8:7924263:CTT:	NC_000005.10:7871150:CTT:	(self)
25368703, 14113608, 10030319, 975961, 6265726, 5353363, 28253503, 14113608, 3130321, ss499021210, ss554162514, ss663622796, ss666298471, ss981223980, ss1373401120, ss1576453599, ss1704552517, ss1704552572, ss1803022825, ss1970006588, ss2030663812, ss2625918064, ss2820907106, ss2996402588, ss3644177995, ss3664292071, ss3732068498, ss3785016870, ss3790435782, ss3795312317, ss3829082457, ss3838003177, ss5170284196, ss5637139163, ss5834488334, ss5965549015, ss5980278316	NC_000005.9:7871263:CTT:	NC_000005.10:7871150:CTT:	(self)
RCV001696316.1, 33336068, 179301326, 12433544, 39768195, 486242556, 256133426, ss3066002002, ss3645858775, ss3647980129, ss3714061346, ss3806205539, ss3843442783, ss3956055543, ss4648864999, ss5262800207, ss5461153229, ss5545810133, ss5705931091, ss5806001352, ss5854671742, ss5892902897	NC_000005.10:7871150:CTT:	NC_000005.10:7871150:CTT:	(self)
ss3255851, ss4475390, ss42512374, ss95385375, ss103705059, ss154944944, ss287766898	NT_006576.16:7861263:CTT:	NC_000005.10:7871150:CTT:	(self)
ss193785756	NT_006576.17:7861150:CTT:	NC_000005.10:7871150:CTT:	(self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs2308000

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:

Select flank length:

Genomic regions, transcripts, and products
Top▲ Help
NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs2308000