Name: rs3048488
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.

rs3048488

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:67049881-67049882 (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: delAT
Variation Type: Deletion
Frequency: delAT=0.041925 (11097/264690, TOPMED)
delAT=0.059299 (14065/237188, GnomAD_exome)
delAT=0.032689 (4582/140170, GnomAD) (+ 13 more)
delAT=0.06222 (6032/96940, ExAC)
delAT=0.21006 (5936/28258, 14KJPN)
delAT=0.03292 (908/27582, ALFA)
delAT=0.21462 (3597/16760, 8.3KJPN)
delAT=0.02621 (328/12512, GO-ESP)
delAT=0.0723 (463/6404, 1000G_30x)
delAT=0.0777 (389/5008, 1000G)
delAT=0.0406 (182/4480, Estonian)
delAT=0.0241 (93/3854, ALSPAC)
delAT=0.0210 (78/3708, TWINSUK)
delAT=0.019 (19/998, GoNL)
delAT=0.010 (6/600, NorthernSweden)
delAT=0.154 (33/214, Vietnamese)

Clinical Significance: Reported in ClinVar
Gene : Consequence: SLC35D1 : 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	27582	AT=0.96708	=0.03292	0.9359	0.00174	0.06236	4
European	Sub	20264	AT=0.97044	=0.02956	0.941571	0.000691	0.057738	0
African	Sub	3506	AT=0.9775	=0.0225	0.956646	0.001711	0.041643	3
African Others	Sub	122	AT=0.984	=0.016	0.967213	0.0	0.032787	0
African American	Sub	3384	AT=0.9772	=0.0228	0.956265	0.001773	0.041962	3
Asian	Sub	168	AT=0.780	=0.220	0.595238	0.035714	0.369048	0
East Asian	Sub	112	AT=0.777	=0.223	0.589286	0.035714	0.375	0
Other Asian	Sub	56	AT=0.79	=0.21	0.607143	0.035714	0.357143	0
Latin American 1	Sub	146	AT=0.938	=0.062	0.876712	0.0	0.123288	0
Latin American 2	Sub	610	AT=0.900	=0.100	0.809836	0.009836	0.180328	0
South Asian	Sub	98	AT=0.95	=0.05	0.918367	0.020408	0.061224	4
Other	Sub	2790	AT=0.9577	=0.0423	0.92043	0.005018	0.074552	5

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	AT=0.958075	delAT=0.041925
gnomAD - Exomes	Global	Study-wide	237188	AT=0.940701	delAT=0.059299
gnomAD - Exomes	European	Sub	126932	AT=0.975325	delAT=0.024675
gnomAD - Exomes	Asian	Sub	46686	AT=0.86953	delAT=0.13047
gnomAD - Exomes	American	Sub	33474	AT=0.88212	delAT=0.11788
gnomAD - Exomes	African	Sub	14574	AT=0.98051	delAT=0.01949
gnomAD - Exomes	Ashkenazi Jewish	Sub	9708	AT=0.9625	delAT=0.0375
gnomAD - Exomes	Other	Sub	5814	AT=0.9573	delAT=0.0427
gnomAD - Genomes	Global	Study-wide	140170	AT=0.967311	delAT=0.032689
gnomAD - Genomes	European	Sub	75902	AT=0.97540	delAT=0.02460
gnomAD - Genomes	African	Sub	42024	AT=0.98032	delAT=0.01968
gnomAD - Genomes	American	Sub	13652	AT=0.92565	delAT=0.07435
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	AT=0.9645	delAT=0.0355
gnomAD - Genomes	East Asian	Sub	3118	AT=0.7870	delAT=0.2130
gnomAD - Genomes	Other	Sub	2154	AT=0.9578	delAT=0.0422
ExAC	Global	Study-wide	96940	AT=0.93778	delAT=0.06222
ExAC	Europe	Sub	57888	AT=0.97196	delAT=0.02804
ExAC	Asian	Sub	20984	AT=0.86537	delAT=0.13463
ExAC	American	Sub	9258	AT=0.8544	delAT=0.1456
ExAC	African	Sub	8060	AT=0.9759	delAT=0.0241
ExAC	Other	Sub	750	AT=0.944	delAT=0.056
14KJPN	JAPANESE	Study-wide	28258	AT=0.78994	delAT=0.21006
Allele Frequency Aggregator	Total	Global	27582	AT=0.96708	delAT=0.03292
Allele Frequency Aggregator	European	Sub	20264	AT=0.97044	delAT=0.02956
Allele Frequency Aggregator	African	Sub	3506	AT=0.9775	delAT=0.0225
Allele Frequency Aggregator	Other	Sub	2790	AT=0.9577	delAT=0.0423
Allele Frequency Aggregator	Latin American 2	Sub	610	AT=0.900	delAT=0.100
Allele Frequency Aggregator	Asian	Sub	168	AT=0.780	delAT=0.220
Allele Frequency Aggregator	Latin American 1	Sub	146	AT=0.938	delAT=0.062
Allele Frequency Aggregator	South Asian	Sub	98	AT=0.95	delAT=0.05
8.3KJPN	JAPANESE	Study-wide	16760	AT=0.78538	delAT=0.21462
GO Exome Sequencing Project	Global	Study-wide	12512	AT=0.97379	delAT=0.02621
GO Exome Sequencing Project	European American	Sub	8250	AT=0.9716	delAT=0.0284
GO Exome Sequencing Project	African American	Sub	4262	AT=0.9779	delAT=0.0221
1000Genomes_30x	Global	Study-wide	6404	AT=0.9277	delAT=0.0723
1000Genomes_30x	African	Sub	1786	AT=0.9888	delAT=0.0112
1000Genomes_30x	Europe	Sub	1266	AT=0.9795	delAT=0.0205
1000Genomes_30x	South Asian	Sub	1202	AT=0.9318	delAT=0.0682
1000Genomes_30x	East Asian	Sub	1170	AT=0.7726	delAT=0.2274
1000Genomes_30x	American	Sub	980	AT=0.930	delAT=0.070
1000Genomes	Global	Study-wide	5008	AT=0.9223	delAT=0.0777
1000Genomes	African	Sub	1322	AT=0.9871	delAT=0.0129
1000Genomes	East Asian	Sub	1008	AT=0.7708	delAT=0.2292
1000Genomes	Europe	Sub	1006	AT=0.9771	delAT=0.0229
1000Genomes	South Asian	Sub	978	AT=0.929	delAT=0.071
1000Genomes	American	Sub	694	AT=0.929	delAT=0.071
Genetic variation in the Estonian population	Estonian	Study-wide	4480	AT=0.9594	delAT=0.0406
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	AT=0.9759	delAT=0.0241
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	AT=0.9790	delAT=0.0210
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	AT=0.981	delAT=0.019
Northern Sweden	ACPOP	Study-wide	600	AT=0.990	delAT=0.010
A Vietnamese Genetic Variation Database	Global	Study-wide	214	AT=0.846	delAT=0.154

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 1	NC_000001.11:g.67049881_67049882del
GRCh37.p13 chr 1	NC_000001.10:g.67515564_67515565del
SLC35D1 RefSeqGene	NG_012933.1:g.9516_9517del

Gene: SLC35D1, solute carrier family 35 member D1 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SLC35D1 transcript	NM_015139.3:c.465-32_465-… NM_015139.3:c.465-32_465-31del	N/A	Intron Variant
SLC35D1 transcript variant X1	XM_006710478.3:c.465-32_4… XM_006710478.3:c.465-32_465-31del	N/A	Intron Variant
SLC35D1 transcript variant X2	XM_047415659.1:c.465-32_4… XM_047415659.1:c.465-32_465-31del	N/A	Intron Variant
SLC35D1 transcript variant X3	XM_047415660.1:c.465-32_4… XM_047415660.1:c.465-32_465-31del	N/A	Intron Variant
SLC35D1 transcript variant X4	XM_047415662.1:c.465-32_4… XM_047415662.1:c.465-32_465-31del	N/A	Intron Variant
SLC35D1 transcript variant X5	XM_047415665.1:c.465-32_4… XM_047415665.1:c.465-32_465-31del	N/A	Intron Variant
SLC35D1 transcript variant X6	XM_047415668.1:c.465-32_4… XM_047415668.1:c.465-32_465-31del	N/A	Intron Variant
SLC35D1 transcript variant X7	XM_047415671.1:c.465-32_4… XM_047415671.1:c.465-32_465-31del	N/A	Intron Variant
SLC35D1 transcript variant X8	XM_047415672.1:c.465-32_4… XM_047415672.1:c.465-32_465-31del	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: delAT (allele ID: 1234417 )

ClinVar Accession	Disease Names	Clinical Significance
RCV001651737.2	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	AT=	delAT
GRCh38.p14 chr 1	NC_000001.11:g.67049881_67049882=	NC_000001.11:g.67049881_67049882del
GRCh37.p13 chr 1	NC_000001.10:g.67515564_67515565=	NC_000001.10:g.67515564_67515565del
SLC35D1 RefSeqGene	NG_012933.1:g.9516_9517=	NG_012933.1:g.9516_9517del
SLC35D1 transcript	NM_015139.2:c.465-31=	NM_015139.2:c.465-32_465-31del
SLC35D1 transcript	NM_015139.3:c.465-31=	NM_015139.3:c.465-32_465-31del
SLC35D1 transcript variant X1	XM_005270665.1:c.465-31=	XM_005270665.1:c.465-32_465-31del
SLC35D1 transcript variant X1	XM_006710478.3:c.465-31=	XM_006710478.3:c.465-32_465-31del
SLC35D1 transcript variant X2	XM_047415659.1:c.465-31=	XM_047415659.1:c.465-32_465-31del
SLC35D1 transcript variant X3	XM_047415660.1:c.465-31=	XM_047415660.1:c.465-32_465-31del
SLC35D1 transcript variant X4	XM_047415662.1:c.465-31=	XM_047415662.1:c.465-32_465-31del
SLC35D1 transcript variant X5	XM_047415665.1:c.465-31=	XM_047415665.1:c.465-32_465-31del
SLC35D1 transcript variant X6	XM_047415668.1:c.465-31=	XM_047415668.1:c.465-32_465-31del
SLC35D1 transcript variant X7	XM_047415671.1:c.465-31=	XM_047415671.1:c.465-32_465-31del
SLC35D1 transcript variant X8	XM_047415672.1:c.465-31=	XM_047415672.1:c.465-32_465-31del

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#.

43 SubSNP, 16 Frequency, 1 ClinVar submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss4279695	Jan 05, 2002 (102)
2	GMI	ss154545490	Dec 01, 2009 (131)
3	GMI	ss287991218	May 04, 2012 (137)
4	1000GENOMES	ss326043814	May 09, 2011 (135)
5	1000GENOMES	ss498885237	May 04, 2012 (137)
6	LUNTER	ss552772680	Apr 25, 2013 (138)
7	SSMP	ss663200306	Apr 01, 2015 (144)
8	BILGI_BIOE	ss666094809	Apr 25, 2013 (138)
9	EVA-GONL	ss975248072	Aug 21, 2014 (142)
10	1000GENOMES	ss1367720998	Aug 21, 2014 (142)
11	EVA_DECODE	ss1584617567	Apr 01, 2015 (144)
12	EVA_UK10K_ALSPAC	ss1700748551	Apr 01, 2015 (144)
13	EVA_UK10K_TWINSUK	ss1700748552	Apr 01, 2015 (144)
14	EVA_EXAC	ss1711621169	Apr 01, 2015 (144)
15	JJLAB	ss2030324606	Sep 14, 2016 (149)
16	SYSTEMSBIOZJU	ss2624386345	Nov 08, 2017 (151)
17	GNOMAD	ss2746351690	Nov 08, 2017 (151)
18	GNOMAD	ss2756090382	Nov 08, 2017 (151)
19	AFFY	ss2984862224	Nov 08, 2017 (151)
20	SWEGEN	ss2986950660	Nov 08, 2017 (151)
21	MCHAISSO	ss3063591753	Nov 08, 2017 (151)
22	ILLUMINA	ss3653634934	Oct 11, 2018 (152)
23	EGCUT_WGS	ss3655020781	Jul 12, 2019 (153)
24	EVA_DECODE	ss3686936089	Jul 12, 2019 (153)
25	ACPOP	ss3727120576	Jul 12, 2019 (153)
26	KHV_HUMAN_GENOMES	ss3799314707	Jul 12, 2019 (153)
27	EVA	ss3823621043	Apr 25, 2020 (154)
28	EVA	ss3826215281	Apr 25, 2020 (154)
29	EVA	ss3986123563	Apr 25, 2021 (155)
30	TOPMED	ss4452684161	Apr 25, 2021 (155)
31	TOMMO_GENOMICS	ss5144324410	Apr 25, 2021 (155)
32	1000G_HIGH_COVERAGE	ss5242559049	Oct 12, 2022 (156)
33	HUGCELL_USP	ss5443593385	Oct 12, 2022 (156)
34	1000G_HIGH_COVERAGE	ss5514981438	Oct 12, 2022 (156)
35	EVA	ss5623993552	Oct 12, 2022 (156)
36	SANFORD_IMAGENETICS	ss5625695388	Oct 12, 2022 (156)
37	TOMMO_GENOMICS	ss5669203657	Oct 12, 2022 (156)
38	YY_MCH	ss5800669381	Oct 12, 2022 (156)
39	EVA	ss5832072338	Oct 12, 2022 (156)
40	EVA	ss5848262849	Oct 12, 2022 (156)
41	EVA	ss5848942225	Oct 12, 2022 (156)
42	EVA	ss5908595653	Oct 12, 2022 (156)
43	EVA	ss5937533933	Oct 12, 2022 (156)
44	1000Genomes	NC_000001.10 - 67515564	Oct 11, 2018 (152)
45	1000Genomes_30x	NC_000001.11 - 67049881	Oct 12, 2022 (156)
46	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 67515564	Oct 11, 2018 (152)
47	Genetic variation in the Estonian population	NC_000001.10 - 67515564	Oct 11, 2018 (152)
48	ExAC	NC_000001.10 - 67515564	Oct 11, 2018 (152)
49	gnomAD - Genomes	NC_000001.11 - 67049881	Apr 25, 2021 (155)
50	gnomAD - Exomes	NC_000001.10 - 67515564	Jul 12, 2019 (153)
51	GO Exome Sequencing Project	NC_000001.10 - 67515564	Oct 11, 2018 (152)
52	Genome of the Netherlands Release 5	NC_000001.10 - 67515564	Apr 25, 2020 (154)
53	Northern Sweden	NC_000001.10 - 67515564	Jul 12, 2019 (153)
54	8.3KJPN	NC_000001.10 - 67515564	Apr 25, 2021 (155)
55	14KJPN	NC_000001.11 - 67049881	Oct 12, 2022 (156)
56	TopMed	NC_000001.11 - 67049881	Apr 25, 2021 (155)
57	UK 10K study - Twins	NC_000001.10 - 67515564	Oct 11, 2018 (152)
58	A Vietnamese Genetic Variation Database	NC_000001.10 - 67515564	Jul 12, 2019 (153)
59	ALFA	NC_000001.11 - 67049881	Apr 25, 2021 (155)
60	ClinVar	RCV001651737.2	Oct 12, 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)
rs35476097	Oct 14, 2006 (127)
rs138593983	Sep 17, 2011 (135)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss287991218, ss326043814, ss552772680, ss1584617567	NC_000001.9:67288151:AT:	NC_000001.11:67049880:AT:	(self)
1956808, 1072013, 759029, 4791228, 584193, 79702, 457526, 405441, 2293717, 1072013, 224582, ss498885237, ss663200306, ss666094809, ss975248072, ss1367720998, ss1700748551, ss1700748552, ss1711621169, ss2030324606, ss2624386345, ss2746351690, ss2756090382, ss2984862224, ss2986950660, ss3653634934, ss3655020781, ss3727120576, ss3823621043, ss3826215281, ss3986123563, ss5144324410, ss5623993552, ss5625695388, ss5832072338, ss5848262849, ss5937533933	NC_000001.10:67515563:AT:	NC_000001.11:67049880:AT:	(self)
RCV001651737.2, 2507373, 13801657, 3040761, 16290496, 11398380861, ss3063591753, ss3686936089, ss3799314707, ss4452684161, ss5242559049, ss5443593385, ss5514981438, ss5669203657, ss5800669381, ss5848942225, ss5908595653	NC_000001.11:67049880:AT:	NC_000001.11:67049880:AT:	(self)
ss4279695, ss154545490	NT_032977.9:37487481:AT:	NC_000001.11:67049880:AT:	(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 rs3048488

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

rs3048488