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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
chr1:16856 (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.

Variation Type
SNV Single Nucleotide Variation
G=0.012388 (1587/128112, GnomAD)
G=0.05388 (903/16760, 8.3KJPN)
G=0.00894 (142/15880, ALFA) (+ 4 more)
G=0.0223 (65/2910, KOREAN)
G=0.006 (3/534, MGP)
A=0.5 (3/6, SGDP_PRJ)
G=0.5 (3/6, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
WASH7P : Splice Donor 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.16856A>G
GRCh37.p13 chr 1 NC_000001.10:g.16856A>G
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 Splice Donor 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 15880 A=0.99106 G=0.00894
European Sub 11876 A=0.98804 G=0.01196
African Sub 2620 A=1.0000 G=0.0000
African Others Sub 102 A=1.000 G=0.000
African American Sub 2518 A=1.0000 G=0.0000
Asian Sub 108 A=1.000 G=0.000
East Asian Sub 84 A=1.00 G=0.00
Other Asian Sub 24 A=1.00 G=0.00
Latin American 1 Sub 140 A=1.000 G=0.000
Latin American 2 Sub 596 A=1.000 G=0.000
South Asian Sub 94 A=1.00 G=0.00
Other Sub 446 A=1.000 G=0.000


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 128112 A=0.987612 G=0.012388
gnomAD - Genomes European Sub 70362 A=0.99144 G=0.00856
gnomAD - Genomes African Sub 37428 A=0.97828 G=0.02172
gnomAD - Genomes American Sub 12392 A=0.99137 G=0.00863
gnomAD - Genomes East Asian Sub 3022 A=0.9997 G=0.0003
gnomAD - Genomes Ashkenazi Jewish Sub 2984 A=0.9873 G=0.0127
gnomAD - Genomes Other Sub 1924 A=0.9865 G=0.0135
8.3KJPN JAPANESE Study-wide 16760 A=0.94612 G=0.05388
KOREAN population from KRGDB KOREAN Study-wide 2910 A=0.9777 G=0.0223
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 A=0.994 G=0.006
SGDP_PRJ Global Study-wide 6 A=0.5 G=0.5

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 A= G
GRCh38.p13 chr 1 NC_000001.11:g.16856= NC_000001.11:g.16856A>G
GRCh37.p13 chr 1 NC_000001.10:g.16856= NC_000001.10:g.16856A>G

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#.

16 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss137077 Oct 10, 2002 (108)
2 SC_SNP ss13428296 Dec 05, 2003 (120)
3 SC_SNP ss15456682 Feb 27, 2004 (120)
4 SC_SNP ss15764817 Feb 27, 2004 (120)
5 HUMANGENOME_JCVI ss95847665 Feb 13, 2009 (131)
6 ENSEMBL ss131807090 Dec 01, 2009 (147)
7 CLINSEQ_SNP ss491581577 May 04, 2012 (144)
8 EVA_MGP ss1710883263 Apr 01, 2015 (144)
9 JJLAB ss2019497469 Sep 14, 2016 (149)
10 GNOMAD ss2750601876 Nov 08, 2017 (151)
11 SWEGEN ss2986141447 Nov 08, 2017 (151)
12 TOPMED ss3066317477 Nov 08, 2017 (151)
13 OMUKHERJEE_ADBS ss3646218032 Oct 11, 2018 (152)
14 SGDP_PRJ ss3847983340 Apr 25, 2020 (154)
15 KRGDB ss3892823049 Apr 25, 2020 (154)
16 TOMMO_GENOMICS ss5142031467 Apr 25, 2021 (155)
17 gnomAD - Genomes NC_000001.11 - 16856 Apr 25, 2021 (155)
18 KOREAN population from KRGDB NC_000001.10 - 16856 Apr 25, 2020 (154)
19 Medical Genome Project healthy controls from Spanish population NC_000001.10 - 16856 Apr 25, 2020 (154)
20 SGDP_PRJ NC_000001.10 - 16856 Apr 25, 2020 (154)
21 8.3KJPN NC_000001.10 - 16856 Apr 25, 2021 (155)
22 ALFA NC_000001.11 - 16856 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)
rs9645447 Feb 27, 2004 (120)
rs62031362 May 25, 2008 (130)
rs71243895 Dec 02, 2009 (131)
rs78815569 Jul 19, 2016 (147)
rs200205172 Jul 01, 2015 (144)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss491581577 NC_000001.9:6718:A:G NC_000001.11:16855:A:G (self)
443, 15, 320, 774, ss1710883263, ss2019497469, ss2750601876, ss2986141447, ss3646218032, ss3847983340, ss3892823049, ss5142031467 NC_000001.10:16855:A:G NC_000001.11:16855:A:G (self)
1563, 13240389156, ss3066317477 NC_000001.11:16855:A:G NC_000001.11:16855:A:G (self)
ss13428296 NT_077402.1:6718:A:G NC_000001.11:16855:A:G (self)
ss137077, ss15456682, ss15764817, ss95847665, ss131807090 NT_077402.2:6855:A:G NC_000001.11:16855:A: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 rs3891260


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