Name: rs3087426
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.

rs3087426

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr8:31141365 (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: delG
Variation Type: Deletion
Frequency: delG=0.052118 (13795/264690, TOPMED)
delG=0.055272 (7751/140234, GnomAD)
delG=0.02488 (703/28258, 14KJPN) (+ 12 more)
delG=0.02387 (400/16760, 8.3KJPN)
delG=0.02196 (333/15162, ALFA)
delG=0.0476 (305/6404, 1000G_30x)
delG=0.0479 (240/5008, 1000G)
delG=0.0732 (328/4480, Estonian)
delG=0.0680 (262/3854, ALSPAC)
delG=0.0650 (241/3708, TWINSUK)
delG=0.0257 (47/1832, Korea1K)
delG=0.068 (68/998, GoNL)
delG=0.043 (26/600, NorthernSweden)
delG=0.037 (8/214, Vietnamese)
delG=0.12 (5/40, GENOME_DK)

Clinical Significance: Reported in ClinVar
Gene : Consequence: WRN : 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	15162	G=0.97804	=0.02196	0.957262	0.001187	0.041551	5
European	Sub	11298	G=0.97053	=0.02947	0.942645	0.001593	0.055762	2
African	Sub	2534	G=1.0000	=0.0000	1.0	0.0	0.0	N/A
African Others	Sub	104	G=1.000	=0.000	1.0	0.0	0.0	N/A
African American	Sub	2430	G=1.0000	=0.0000	1.0	0.0	0.0	N/A
Asian	Sub	104	G=1.000	=0.000	1.0	0.0	0.0	N/A
East Asian	Sub	80	G=1.00	=0.00	1.0	0.0	0.0	N/A
Other Asian	Sub	24	G=1.00	=0.00	1.0	0.0	0.0	N/A
Latin American 1	Sub	130	G=1.000	=0.000	1.0	0.0	0.0	N/A
Latin American 2	Sub	576	G=1.000	=0.000	1.0	0.0	0.0	N/A
South Asian	Sub	86	G=1.00	=0.00	1.0	0.0	0.0	N/A
Other	Sub	434	G=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	G=0.947882	delG=0.052118
gnomAD - Genomes	Global	Study-wide	140234	G=0.944728	delG=0.055272
gnomAD - Genomes	European	Sub	75934	G=0.93673	delG=0.06327
gnomAD - Genomes	African	Sub	42032	G=0.94970	delG=0.05030
gnomAD - Genomes	American	Sub	13664	G=0.96363	delG=0.03637
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	G=0.9524	delG=0.0476
gnomAD - Genomes	East Asian	Sub	3132	G=0.9754	delG=0.0246
gnomAD - Genomes	Other	Sub	2150	G=0.9530	delG=0.0470
14KJPN	JAPANESE	Study-wide	28258	G=0.97512	delG=0.02488
8.3KJPN	JAPANESE	Study-wide	16760	G=0.97613	delG=0.02387
Allele Frequency Aggregator	Total	Global	15162	G=0.97804	delG=0.02196
Allele Frequency Aggregator	European	Sub	11298	G=0.97053	delG=0.02947
Allele Frequency Aggregator	African	Sub	2534	G=1.0000	delG=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	576	G=1.000	delG=0.000
Allele Frequency Aggregator	Other	Sub	434	G=1.000	delG=0.000
Allele Frequency Aggregator	Latin American 1	Sub	130	G=1.000	delG=0.000
Allele Frequency Aggregator	Asian	Sub	104	G=1.000	delG=0.000
Allele Frequency Aggregator	South Asian	Sub	86	G=1.00	delG=0.00
1000Genomes_30x	Global	Study-wide	6404	G=0.9524	delG=0.0476
1000Genomes_30x	African	Sub	1786	G=0.9513	delG=0.0487
1000Genomes_30x	Europe	Sub	1266	G=0.9415	delG=0.0585
1000Genomes_30x	South Asian	Sub	1202	G=0.9176	delG=0.0824
1000Genomes_30x	East Asian	Sub	1170	G=0.9786	delG=0.0214
1000Genomes_30x	American	Sub	980	G=0.980	delG=0.020
1000Genomes	Global	Study-wide	5008	G=0.9521	delG=0.0479
1000Genomes	African	Sub	1322	G=0.9546	delG=0.0454
1000Genomes	East Asian	Sub	1008	G=0.9762	delG=0.0238
1000Genomes	Europe	Sub	1006	G=0.9423	delG=0.0577
1000Genomes	South Asian	Sub	978	G=0.915	delG=0.085
1000Genomes	American	Sub	694	G=0.978	delG=0.022
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.9268	delG=0.0732
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.9320	delG=0.0680
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.9350	delG=0.0650
Korean Genome Project	KOREAN	Study-wide	1832	G=0.9743	delG=0.0257
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.932	delG=0.068
Northern Sweden	ACPOP	Study-wide	600	G=0.957	delG=0.043
A Vietnamese Genetic Variation Database	Global	Study-wide	214	G=0.963	delG=0.037
The Danish reference pan genome	Danish	Study-wide	40	G=0.88	delG=0.12

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 8	NC_000008.11:g.31141365del
GRCh37.p13 chr 8	NC_000008.10:g.30998881del
WRN RefSeqGene (LRG_524)	NG_008870.1:g.113104del

Gene: WRN, WRN RecQ like helicase (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
WRN transcript	NM_000553.6:c.2968-65del	N/A	Intron Variant
WRN transcript variant X1	XM_011544639.4:c.2887-65d… XM_011544639.4:c.2887-65del	N/A	Intron Variant
WRN transcript variant X5	XM_011544640.2:c.1369-65d… XM_011544640.2:c.1369-65del	N/A	Intron Variant
WRN transcript variant X2	XR_949470.4:n.	N/A	Intron Variant
WRN transcript variant X3	XR_949471.4:n.	N/A	Intron Variant
WRN transcript variant X4	XR_949472.4:n.	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: delG (allele ID: 1262156 )

ClinVar Accession	Disease Names	Clinical Significance
RCV001686847.1	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	G=	delG
GRCh38.p14 chr 8	NC_000008.11:g.31141365=	NC_000008.11:g.31141365del
GRCh37.p13 chr 8	NC_000008.10:g.30998881=	NC_000008.10:g.30998881del
WRN RefSeqGene (LRG_524)	NG_008870.1:g.113104=	NG_008870.1:g.113104del
WRN transcript	NM_000553.4:c.2968-65=	NM_000553.4:c.2968-65del
WRN transcript	NM_000553.6:c.2968-65=	NM_000553.6:c.2968-65del
WRN transcript variant X1	XM_005273632.1:c.2887-65=	XM_005273632.1:c.2887-65del
WRN transcript variant X1	XM_011544639.4:c.2887-65=	XM_011544639.4:c.2887-65del
WRN transcript variant X5	XM_011544640.2:c.1369-65=	XM_011544640.2:c.1369-65del

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#.

39 SubSNP, 15 Frequency, 1 ClinVar submissions

No	Submitter	Submission ID	Date (Build)
1	UWGC	ss4318976	Jan 05, 2002 (102)
2	EGP_SNPS	ss16359557	Feb 27, 2004 (120)
3	1000GENOMES	ss327099578	May 09, 2011 (137)
4	1000GENOMES	ss500149830	May 04, 2012 (137)
5	LUNTER	ss551833642	Apr 25, 2013 (138)
6	LUNTER	ss552051258	Apr 25, 2013 (138)
7	TISHKOFF	ss554386235	Apr 25, 2013 (138)
8	SSMP	ss663848686	Apr 01, 2015 (144)
9	EVA-GONL	ss985362537	Aug 21, 2014 (142)
10	1000GENOMES	ss1367890517	Aug 21, 2014 (142)
11	EVA_GENOME_DK	ss1577182749	Apr 01, 2015 (144)
12	EVA_DECODE	ss1594957229	Apr 01, 2015 (144)
13	EVA_UK10K_ALSPAC	ss1706003015	Apr 01, 2015 (144)
14	EVA_UK10K_TWINSUK	ss1706003318	Apr 01, 2015 (144)
15	JJLAB	ss2030901047	Sep 14, 2016 (149)
16	GNOMAD	ss2865051219	Nov 08, 2017 (151)
17	SWEGEN	ss3002941384	Nov 08, 2017 (151)
18	MCHAISSO	ss3066195871	Nov 08, 2017 (151)
19	BEROUKHIMLAB	ss3644259256	Oct 12, 2018 (152)
20	EGCUT_WGS	ss3670627481	Jul 13, 2019 (153)
21	EVA_DECODE	ss3721729709	Jul 13, 2019 (153)
22	ACPOP	ss3735543183	Jul 13, 2019 (153)
23	KHV_HUMAN_GENOMES	ss3810987025	Jul 13, 2019 (153)
24	EVA	ss3839059295	Apr 26, 2020 (154)
25	EVA	ss3844517718	Apr 26, 2020 (154)
26	KOGIC	ss3963577903	Apr 26, 2020 (154)
27	EVA	ss3986419883	Apr 26, 2021 (155)
28	TOPMED	ss4780970997	Apr 26, 2021 (155)
29	TOMMO_GENOMICS	ss5188037086	Apr 26, 2021 (155)
30	1000G_HIGH_COVERAGE	ss5276630157	Oct 16, 2022 (156)
31	HUGCELL_USP	ss5473253331	Oct 16, 2022 (156)
32	1000G_HIGH_COVERAGE	ss5566698943	Oct 16, 2022 (156)
33	SANFORD_IMAGENETICS	ss5645094790	Oct 16, 2022 (156)
34	TOMMO_GENOMICS	ss5729765554	Oct 16, 2022 (156)
35	YY_MCH	ss5809590207	Oct 16, 2022 (156)
36	EVA	ss5830340913	Oct 16, 2022 (156)
37	EVA	ss5848704840	Oct 16, 2022 (156)
38	EVA	ss5888370832	Oct 16, 2022 (156)
39	EVA	ss5974284571	Oct 16, 2022 (156)
40	1000Genomes	NC_000008.10 - 30998881	Oct 12, 2018 (152)
41	1000Genomes_30x	NC_000008.11 - 31141365	Oct 16, 2022 (156)
42	The Avon Longitudinal Study of Parents and Children	NC_000008.10 - 30998881	Oct 12, 2018 (152)
43	Genetic variation in the Estonian population	NC_000008.10 - 30998881	Oct 12, 2018 (152)
44	The Danish reference pan genome	NC_000008.10 - 30998881	Apr 26, 2020 (154)
45	gnomAD - Genomes	NC_000008.11 - 31141365	Apr 26, 2021 (155)
46	Genome of the Netherlands Release 5	NC_000008.10 - 30998881	Apr 26, 2020 (154)
47	Korean Genome Project	NC_000008.11 - 31141365	Apr 26, 2020 (154)
48	Northern Sweden	NC_000008.10 - 30998881	Jul 13, 2019 (153)
49	8.3KJPN	NC_000008.10 - 30998881	Apr 26, 2021 (155)
50	14KJPN	NC_000008.11 - 31141365	Oct 16, 2022 (156)
51	TopMed	NC_000008.11 - 31141365	Apr 26, 2021 (155)
52	UK 10K study - Twins	NC_000008.10 - 30998881	Oct 12, 2018 (152)
53	A Vietnamese Genetic Variation Database	NC_000008.10 - 30998881	Jul 13, 2019 (153)
54	ALFA	NC_000008.11 - 31141365	Apr 26, 2021 (155)
55	ClinVar	RCV001686847.1	Oct 16, 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)
rs148358108	May 04, 2012 (137)
rs373161349	May 13, 2013 (138)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss327099578, ss551833642, ss552051258, ss1594957229	NC_000008.9:31118422:G:	NC_000008.11:31141364:G:	(self)
41363558, 23001392, 16365729, 1211947, 10274599, 8828048, 46006393, 23001392, 5128012, ss500149830, ss554386235, ss663848686, ss985362537, ss1367890517, ss1577182749, ss1706003015, ss1706003318, ss2030901047, ss2865051219, ss3002941384, ss3644259256, ss3670627481, ss3735543183, ss3839059295, ss3986419883, ss5188037086, ss5645094790, ss5830340913, ss5848704840, ss5974284571	NC_000008.10:30998880:G:	NC_000008.11:31141364:G:	(self)
RCV001686847.1, 54224878, 291638096, 19955904, 63602658, 618348557, 6918546507, ss3066195871, ss3721729709, ss3810987025, ss3844517718, ss3963577903, ss4780970997, ss5276630157, ss5473253331, ss5566698943, ss5729765554, ss5809590207, ss5888370832	NC_000008.11:31141364:G:	NC_000008.11:31141364:G:	(self)
ss4318976, ss16359557	NT_167187.1:18857026:G:	NC_000008.11:31141364:G:	(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 rs3087426

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
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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.
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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs3087426