Name: rs3058458
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.

rs3058458

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr5:74726281-74726284 (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: delAGAG
Variation Type: Deletion
Frequency: delAGAG=0.168167 (44512/264690, TOPMED)
delAGAG=0.164395 (22986/139822, GnomAD)
delAGAG=0.00679 (192/28258, 14KJPN) (+ 12 more)
delAGAG=0.00722 (121/16760, 8.3KJPN)
delAGAG=0.02918 (422/14460, ALFA)
delAGAG=0.1452 (930/6404, 1000G_30x)
delAGAG=0.1398 (700/5008, 1000G)
delAGAG=0.0949 (425/4480, Estonian)
delAGAG=0.1256 (484/3854, ALSPAC)
delAGAG=0.1321 (490/3708, TWINSUK)
delAGAG=0.0147 (27/1832, Korea1K)
delAGAG=0.127 (127/998, GoNL)
delAGAG=0.088 (53/600, NorthernSweden)
delAGAG=0.009 (2/214, Vietnamese)
delAGAG=0.07 (3/40, GENOME_DK)

Clinical Significance: Reported in ClinVar
Gene : Consequence: GFM2 : 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	14460	AGAG=0.97082	=0.02918	0.943845	0.002213	0.053942	10
European	Sub	11868	AGAG=0.96444	=0.03556	0.931581	0.002696	0.065723	6
African	Sub	1478	AGAG=1.0000	=0.0000	1.0	0.0	0.0	N/A
African Others	Sub	64	AGAG=1.00	=0.00	1.0	0.0	0.0	N/A
African American	Sub	1414	AGAG=1.0000	=0.0000	1.0	0.0	0.0	N/A
Asian	Sub	102	AGAG=1.000	=0.000	1.0	0.0	0.0	N/A
East Asian	Sub	80	AGAG=1.00	=0.00	1.0	0.0	0.0	N/A
Other Asian	Sub	22	AGAG=1.00	=0.00	1.0	0.0	0.0	N/A
Latin American 1	Sub	92	AGAG=1.00	=0.00	1.0	0.0	0.0	N/A
Latin American 2	Sub	478	AGAG=1.000	=0.000	1.0	0.0	0.0	N/A
South Asian	Sub	72	AGAG=1.00	=0.00	1.0	0.0	0.0	N/A
Other	Sub	370	AGAG=1.000	=0.000	1.0	0.0	0.0	N/A

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	AGAG=0.831833	delAGAG=0.168167
gnomAD - Genomes	Global	Study-wide	139822	AGAG=0.835605	delAGAG=0.164395
gnomAD - Genomes	European	Sub	75796	AGAG=0.88015	delAGAG=0.11985
gnomAD - Genomes	African	Sub	41806	AGAG=0.72992	delAGAG=0.27008
gnomAD - Genomes	American	Sub	13620	AGAG=0.87643	delAGAG=0.12357
gnomAD - Genomes	Ashkenazi Jewish	Sub	3318	AGAG=0.8469	delAGAG=0.1531
gnomAD - Genomes	East Asian	Sub	3130	AGAG=0.9764	delAGAG=0.0236
gnomAD - Genomes	Other	Sub	2152	AGAG=0.8392	delAGAG=0.1608
14KJPN	JAPANESE	Study-wide	28258	AGAG=0.99321	delAGAG=0.00679
8.3KJPN	JAPANESE	Study-wide	16760	AGAG=0.99278	delAGAG=0.00722
Allele Frequency Aggregator	Total	Global	14460	AGAG=0.97082	delAGAG=0.02918
Allele Frequency Aggregator	European	Sub	11868	AGAG=0.96444	delAGAG=0.03556
Allele Frequency Aggregator	African	Sub	1478	AGAG=1.0000	delAGAG=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	478	AGAG=1.000	delAGAG=0.000
Allele Frequency Aggregator	Other	Sub	370	AGAG=1.000	delAGAG=0.000
Allele Frequency Aggregator	Asian	Sub	102	AGAG=1.000	delAGAG=0.000
Allele Frequency Aggregator	Latin American 1	Sub	92	AGAG=1.00	delAGAG=0.00
Allele Frequency Aggregator	South Asian	Sub	72	AGAG=1.00	delAGAG=0.00
1000Genomes_30x	Global	Study-wide	6404	AGAG=0.8548	delAGAG=0.1452
1000Genomes_30x	African	Sub	1786	AGAG=0.7172	delAGAG=0.2828
1000Genomes_30x	Europe	Sub	1266	AGAG=0.8602	delAGAG=0.1398
1000Genomes_30x	South Asian	Sub	1202	AGAG=0.9151	delAGAG=0.0849
1000Genomes_30x	East Asian	Sub	1170	AGAG=0.9786	delAGAG=0.0214
1000Genomes_30x	American	Sub	980	AGAG=0.877	delAGAG=0.123
1000Genomes	Global	Study-wide	5008	AGAG=0.8602	delAGAG=0.1398
1000Genomes	African	Sub	1322	AGAG=0.7148	delAGAG=0.2852
1000Genomes	East Asian	Sub	1008	AGAG=0.9792	delAGAG=0.0208
1000Genomes	Europe	Sub	1006	AGAG=0.8618	delAGAG=0.1382
1000Genomes	South Asian	Sub	978	AGAG=0.918	delAGAG=0.082
1000Genomes	American	Sub	694	AGAG=0.880	delAGAG=0.120
Genetic variation in the Estonian population	Estonian	Study-wide	4480	AGAG=0.9051	delAGAG=0.0949
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	AGAG=0.8744	delAGAG=0.1256
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	AGAG=0.8679	delAGAG=0.1321
Korean Genome Project	KOREAN	Study-wide	1832	AGAG=0.9853	delAGAG=0.0147
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	AGAG=0.873	delAGAG=0.127
Northern Sweden	ACPOP	Study-wide	600	AGAG=0.912	delAGAG=0.088
A Vietnamese Genetic Variation Database	Global	Study-wide	214	AGAG=0.991	delAGAG=0.009
The Danish reference pan genome	Danish	Study-wide	40	AGAG=0.93	delAGAG=0.07

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.74726281_74726284del
GRCh37.p13 chr 5	NC_000005.9:g.74022106_74022109del
GFM2 RefSeqGene	NG_011531.1:g.45934_45937del

Gene: GFM2, GTP dependent ribosome recycling factor mitochondrial 2 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
GFM2 transcript variant 4	NM_001281302.2:c.1823-158… NM_001281302.2:c.1823-158_1823-155del	N/A	Intron Variant
GFM2 transcript variant 1	NM_032380.5:c.1727-158_17… NM_032380.5:c.1727-158_1727-155del	N/A	Intron Variant
GFM2 transcript variant 2	NM_170691.3:c.1586-158_15… NM_170691.3:c.1586-158_1586-155del	N/A	Intron Variant
GFM2 transcript variant 3	NM_170681.3:c.	N/A	Genic Downstream Transcript Variant
GFM2 transcript variant 5	NR_104006.2:n.	N/A	Intron Variant
GFM2 transcript variant X2	XM_017009986.2:c.1727-158… XM_017009986.2:c.1727-158_1727-155del	N/A	Intron Variant
GFM2 transcript variant X1	XM_047417833.1:c.1727-158… XM_047417833.1:c.1727-158_1727-155del	N/A	Intron Variant
GFM2 transcript variant X3	XM_047417834.1:c.1586-158… XM_047417834.1:c.1586-158_1586-155del	N/A	Intron Variant
GFM2 transcript variant X4	XM_047417835.1:c.1586-158… XM_047417835.1:c.1586-158_1586-155del	N/A	Intron Variant
GFM2 transcript variant X5	XM_011543691.4:c.	N/A	Genic Downstream Transcript 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: delAGAG (allele ID: 1281212 )

ClinVar Accession	Disease Names	Clinical Significance
RCV001713369.1	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	AGAG=	delAGAG
GRCh38.p14 chr 5	NC_000005.10:g.74726281_74726284=	NC_000005.10:g.74726281_74726284del
GRCh37.p13 chr 5	NC_000005.9:g.74022106_74022109=	NC_000005.9:g.74022106_74022109del
GFM2 RefSeqGene	NG_011531.1:g.45934_45937=	NG_011531.1:g.45934_45937del
GFM2 transcript variant 4	NM_001281302.1:c.1823-155=	NM_001281302.1:c.1823-158_1823-155del
GFM2 transcript variant 4	NM_001281302.2:c.1823-155=	NM_001281302.2:c.1823-158_1823-155del
GFM2 transcript variant 1	NM_032380.4:c.1727-155=	NM_032380.4:c.1727-158_1727-155del
GFM2 transcript variant 1	NM_032380.5:c.1727-155=	NM_032380.5:c.1727-158_1727-155del
GFM2 transcript variant 2	NM_170691.2:c.1586-155=	NM_170691.2:c.1586-158_1586-155del
GFM2 transcript variant 2	NM_170691.3:c.1586-155=	NM_170691.3:c.1586-158_1586-155del
GFM2 transcript variant X2	XM_017009986.2:c.1727-155=	XM_017009986.2:c.1727-158_1727-155del
GFM2 transcript variant X1	XM_047417833.1:c.1727-155=	XM_047417833.1:c.1727-158_1727-155del
GFM2 transcript variant X3	XM_047417834.1:c.1586-155=	XM_047417834.1:c.1586-158_1586-155del
GFM2 transcript variant X4	XM_047417835.1:c.1586-155=	XM_047417835.1:c.1586-158_1586-155del

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#.

44 SubSNP, 15 Frequency, 1 ClinVar submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss4289749	Jan 05, 2002 (102)
2	1000GENOMES	ss326680677	May 09, 2011 (135)
3	1000GENOMES	ss326720290	May 09, 2011 (135)
4	1000GENOMES	ss326931906	May 09, 2011 (135)
5	1000GENOMES	ss499153230	May 04, 2012 (137)
6	LUNTER	ss551508605	Apr 25, 2013 (138)
7	LUNTER	ss551666872	Apr 25, 2013 (138)
8	TISHKOFF	ss554192653	Apr 25, 2013 (138)
9	SSMP	ss663619865	Apr 01, 2015 (144)
10	BILGI_BIOE	ss666314566	Apr 25, 2013 (138)
11	EVA-GONL	ss981696054	Aug 21, 2014 (142)
12	1000GENOMES	ss1373957844	Aug 21, 2014 (142)
13	EVA_GENOME_DK	ss1576537153	Apr 01, 2015 (144)
14	EVA_DECODE	ss1591215500	Apr 01, 2015 (144)
15	EVA_UK10K_ALSPAC	ss1704720316	Apr 01, 2015 (144)
16	EVA_UK10K_TWINSUK	ss1704720345	Apr 01, 2015 (144)
17	HAMMER_LAB	ss1803683682	Sep 08, 2015 (146)
18	JJLAB	ss2030690987	Sep 14, 2016 (149)
19	GNOMAD	ss2826071507	Nov 08, 2017 (151)
20	SWEGEN	ss2997139367	Nov 08, 2017 (151)
21	MCHAISSO	ss3065035558	Nov 08, 2017 (151)
22	BEROUKHIMLAB	ss3644187722	Oct 12, 2018 (152)
23	BIOINF_KMB_FNS_UNIBA	ss3645885625	Oct 12, 2018 (152)
24	EGCUT_WGS	ss3665017256	Jul 13, 2019 (153)
25	EVA_DECODE	ss3714924167	Jul 13, 2019 (153)
26	ACPOP	ss3732463260	Jul 13, 2019 (153)
27	KHV_HUMAN_GENOMES	ss3806746616	Jul 13, 2019 (153)
28	EVA	ss3829305805	Apr 26, 2020 (154)
29	EVA	ss3838126811	Apr 26, 2020 (154)
30	EVA	ss3843567623	Apr 26, 2020 (154)
31	KOGIC	ss3956912602	Apr 26, 2020 (154)
32	TOPMED	ss4664330374	Apr 26, 2021 (155)
33	TOMMO_GENOMICS	ss5172320977	Apr 26, 2021 (155)
34	1000G_HIGH_COVERAGE	ss5264413877	Oct 13, 2022 (156)
35	HUGCELL_USP	ss5462543830	Oct 13, 2022 (156)
36	1000G_HIGH_COVERAGE	ss5548294675	Oct 13, 2022 (156)
37	SANFORD_IMAGENETICS	ss5638057199	Oct 13, 2022 (156)
38	TOMMO_GENOMICS	ss5708882515	Oct 13, 2022 (156)
39	YY_MCH	ss5806427212	Oct 13, 2022 (156)
40	EVA	ss5835096050	Oct 13, 2022 (156)
41	EVA	ss5854862687	Oct 13, 2022 (156)
42	EVA	ss5894683079	Oct 13, 2022 (156)
43	EVA	ss5966487083	Oct 13, 2022 (156)
44	EVA	ss5980300316	Oct 13, 2022 (156)
45	1000Genomes	NC_000005.9 - 74022106	Oct 12, 2018 (152)
46	1000Genomes_30x	NC_000005.10 - 74726281	Oct 13, 2022 (156)
47	The Avon Longitudinal Study of Parents and Children	NC_000005.9 - 74022106	Oct 12, 2018 (152)
48	Genetic variation in the Estonian population	NC_000005.9 - 74022106	Oct 12, 2018 (152)
49	The Danish reference pan genome	NC_000005.9 - 74022106	Apr 26, 2020 (154)
50	gnomAD - Genomes	NC_000005.10 - 74726281	Apr 26, 2021 (155)
51	Genome of the Netherlands Release 5	NC_000005.9 - 74022106	Apr 26, 2020 (154)
52	Korean Genome Project	NC_000005.10 - 74726281	Apr 26, 2020 (154)
53	Northern Sweden	NC_000005.9 - 74022106	Jul 13, 2019 (153)
54	8.3KJPN	NC_000005.9 - 74022106	Apr 26, 2021 (155)
55	14KJPN	NC_000005.10 - 74726281	Oct 13, 2022 (156)
56	TopMed	NC_000005.10 - 74726281	Apr 26, 2021 (155)
57	UK 10K study - Twins	NC_000005.9 - 74022106	Oct 12, 2018 (152)
58	A Vietnamese Genetic Variation Database	NC_000005.9 - 74022106	Jul 13, 2019 (153)
59	ALFA	NC_000005.10 - 74726281	Apr 26, 2021 (155)
60	ClinVar	RCV001713369.1	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)
rs146799824	Sep 17, 2011 (135)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss326680677, ss326720290, ss326931906, ss551508605, ss551666872, ss1591215500	NC_000005.8:74057861:AGAG:	NC_000005.10:74726280:AGAG:	(self)
27211500, 15129238, 10755504, 1003530, 6725798, 5748125, 30290284, 15129238, 3358410, ss499153230, ss554192653, ss663619865, ss666314566, ss981696054, ss1373957844, ss1576537153, ss1704720316, ss1704720345, ss1803683682, ss2030690987, ss2826071507, ss2997139367, ss3644187722, ss3665017256, ss3732463260, ss3829305805, ss3838126811, ss5172320977, ss5638057199, ss5835096050, ss5966487083, ss5980300316	NC_000005.9:74022105:AGAG:	NC_000005.10:74726280:AGAG:	(self)
RCV001713369.1, 35820610, 192357261, 13290603, 42719619, 501707931, 6832761310, ss3065035558, ss3645885625, ss3714924167, ss3806746616, ss3843567623, ss3956912602, ss4664330374, ss5264413877, ss5462543830, ss5548294675, ss5708882515, ss5806427212, ss5854862687, ss5894683079	NC_000005.10:74726280:AGAG:	NC_000005.10:74726280:AGAG:	(self)
ss4289749	NT_006713.15:24616464:AGAG:	NC_000005.10:74726280:AGAG:	(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 rs3058458

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs3058458