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dbSNP Short Genetic Variations

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.


Current Build 155

Released April 9, 2021

Homo sapiens
chr1:16534 (GRCh38.p13) 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.

C>A / C>G / C>T
Variation Type
SNV Single Nucleotide Variation
A=0.000068 (8/118234, GnomAD)
T=0.44761 (7502/16760, 8.3KJPN)
T=0.19368 (2244/11586, ALFA) (+ 3 more)
T=0.4353 (1272/2922, KOREAN)
C=0.500 (265/530, SGDP_PRJ)
T=0.500 (265/530, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
WASH7P : Intron Variant
0 citations
Genomic View
See rs on genome

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.p13 chr 1 NC_000001.11:g.16534C>A
GRCh38.p13 chr 1 NC_000001.11:g.16534C>G
GRCh38.p13 chr 1 NC_000001.11:g.16534C>T
GRCh37.p13 chr 1 NC_000001.10:g.16534C>A
GRCh37.p13 chr 1 NC_000001.10:g.16534C>G
GRCh37.p13 chr 1 NC_000001.10:g.16534C>T
Gene: WASH7P, WASP family homolog 7, pseudogene (minus strand)
Molecule type Change Amino acid[Codon] SO Term
WASH7P transcript NR_024540.1: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.

Not Reported in ClinVar

ALFA Allele Frequency (New)
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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 11586 C=0.80632 A=0.00000, G=0.00000, T=0.19368
European Sub 8608 C=0.7398 A=0.0000, G=0.0000, T=0.2602
African Sub 2030 C=1.0000 A=0.0000, G=0.0000, T=0.0000
African Others Sub 88 C=1.00 A=0.00, G=0.00, T=0.00
African American Sub 1942 C=1.0000 A=0.0000, G=0.0000, T=0.0000
Asian Sub 104 C=1.000 A=0.000, G=0.000, T=0.000
East Asian Sub 82 C=1.00 A=0.00, G=0.00, T=0.00
Other Asian Sub 22 C=1.00 A=0.00, G=0.00, T=0.00
Latin American 1 Sub 102 C=1.000 A=0.000, G=0.000, T=0.000
Latin American 2 Sub 356 C=1.000 A=0.000, G=0.000, T=0.000
South Asian Sub 76 C=1.00 A=0.00, G=0.00, T=0.00
Other Sub 310 C=0.987 A=0.000, G=0.000, T=0.013


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").

Study Population Group Sample Size Ref Allele Alt Allele
gnomAD - Genomes Global Study-wide 118234 C=0.999932 A=0.000068
gnomAD - Genomes European Sub 64848 C=0.99989 A=0.00011
gnomAD - Genomes African Sub 34446 C=0.99997 A=0.00003
gnomAD - Genomes American Sub 11340 C=1.00000 A=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 2922 C=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 2892 C=1.0000 A=0.0000
gnomAD - Genomes Other Sub 1786 C=1.0000 A=0.0000
8.3KJPN JAPANESE Study-wide 16760 C=0.55239 T=0.44761
KOREAN population from KRGDB KOREAN Study-wide 2922 C=0.5647 T=0.4353
SGDP_PRJ Global Study-wide 530 C=0.500 T=0.500

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 C= A G T
GRCh38.p13 chr 1 NC_000001.11:g.16534= NC_000001.11:g.16534C>A NC_000001.11:g.16534C>G NC_000001.11:g.16534C>T
GRCh37.p13 chr 1 NC_000001.10:g.16534= NC_000001.10:g.16534C>A NC_000001.10:g.16534C>G NC_000001.10:g.16534C>T

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#.

25 SubSNP, 5 Frequency submissions
No Submitter Submission ID Date (Build)
1 CGAP-GAI ss18056 Sep 19, 2000 (52)
2 CSHL-HAPMAP ss19117769 Feb 28, 2004 (130)
3 SEQUENOM ss24780910 Sep 20, 2004 (126)
4 SSAHASNP ss35520519 May 24, 2005 (130)
5 BCMHGSC_JDW ss87152799 Mar 25, 2008 (130)
6 HUMANGENOME_JCVI ss95847667 Feb 13, 2009 (131)
7 ENSEMBL ss132365286 Dec 01, 2009 (131)
8 ENSEMBL ss138921412 Dec 01, 2009 (131)
9 ENSEMBL ss144260586 Dec 01, 2009 (131)
10 ENSEMBL ss144277618 Dec 01, 2009 (131)
11 GMI ss154521904 Dec 01, 2009 (131)
12 GMI ss275679867 May 04, 2012 (144)
13 GMI ss283987239 Apr 25, 2013 (144)
14 BILGI_BIOE ss538305546 Apr 25, 2013 (144)
15 GRF ss2697372903 Nov 08, 2017 (151)
16 GNOMAD ss2750601793 Nov 08, 2017 (151)
17 SWEGEN ss2986141424 Nov 08, 2017 (151)
18 TOPMED ss3066317368 Nov 08, 2017 (151)
19 TOPMED ss3066317369 Nov 08, 2017 (151)
20 CSHL ss3343271469 Nov 08, 2017 (151)
21 OMUKHERJEE_ADBS ss3646218021 Oct 11, 2018 (152)
22 URBANLAB ss3646580258 Oct 11, 2018 (152)
23 SGDP_PRJ ss3847983325 Apr 25, 2020 (154)
24 KRGDB ss3892823017 Apr 25, 2020 (154)
25 TOMMO_GENOMICS ss5142031411 Apr 25, 2021 (155)
26 gnomAD - Genomes NC_000001.11 - 16534 Apr 25, 2021 (155)
27 KOREAN population from KRGDB NC_000001.10 - 16534 Apr 25, 2020 (154)
28 SGDP_PRJ NC_000001.10 - 16534 Apr 25, 2020 (154)
29 8.3KJPN NC_000001.10 - 16534 Apr 25, 2021 (155)
30 ALFA NC_000001.11 - 16534 Apr 25, 2021 (155)

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)
rs12405068 May 24, 2008 (130)
rs17343997 May 23, 2006 (127)
rs62636499 May 24, 2008 (130)
rs71243897 Dec 02, 2009 (131)
rs201459529 Jul 01, 2015 (144)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
1468, 7520046421, ss3066317368 NC_000001.11:16533:C:A NC_000001.11:16533:C:A (self)
7520046421 NC_000001.11:16533:C:G NC_000001.11:16533:C:G
ss35520519 NC_000001.8:6396:C:T NC_000001.11:16533:C:T (self)
ss87152799, ss275679867, ss283987239 NC_000001.9:6396:C:T NC_000001.11:16533:C:T (self)
411, 305, 718, ss538305546, ss2697372903, ss2750601793, ss2986141424, ss3343271469, ss3646218021, ss3847983325, ss3892823017, ss5142031411 NC_000001.10:16533:C:T NC_000001.11:16533:C:T (self)
7520046421, ss3066317369, ss3646580258 NC_000001.11:16533:C:T NC_000001.11:16533:C:T (self)
ss19117769 NT_077402.1:6396:C:T NC_000001.11:16533:C:T (self)
ss18056, ss24780910, ss95847667, ss132365286, ss138921412, ss144260586, ss144277618, ss154521904 NT_077402.2:6533:C:T NC_000001.11:16533:C:T (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 rs15642


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.

Software version is: 2.0.1.post596+ae089ad