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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.

rs6682385

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:14930 (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.

Alleles
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.42725 (7159/16756, 8.3KJPN)
G=0.38085 (6220/16332, ALFA)
G=0.4822 (2415/5008, 1000G) (+ 3 more)
G=0.4201 (1231/2930, KOREAN)
G=0.333 (178/534, MGP)
A=0.481 (253/526, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
WASH7P : Intron Variant
Publications
0 citations
Genomic View
See rs on genome
Help

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.14930A>G
GRCh37.p13 chr 1 NC_000001.10:g.14930A>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 Intron Variant
Help

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
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 16332 A=0.61915 G=0.38085
European Sub 12080 A=0.57765 G=0.42235
African Sub 2816 A=0.7617 G=0.2383
African Others Sub 108 A=0.843 G=0.157
African American Sub 2708 A=0.7585 G=0.2415
Asian Sub 108 A=0.926 G=0.074
East Asian Sub 84 A=0.93 G=0.07
Other Asian Sub 24 A=0.92 G=0.08
Latin American 1 Sub 146 A=0.699 G=0.301
Latin American 2 Sub 610 A=0.630 G=0.370
South Asian Sub 94 A=0.73 G=0.27
Other Sub 478 A=0.699 G=0.301


Help

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").

Download
Study Population Group Sample Size Ref Allele Alt Allele
8.3KJPN JAPANESE Study-wide 16756 A=0.57275 G=0.42725
Allele Frequency Aggregator Total Global 16332 A=0.61915 G=0.38085
Allele Frequency Aggregator European Sub 12080 A=0.57765 G=0.42235
Allele Frequency Aggregator African Sub 2816 A=0.7617 G=0.2383
Allele Frequency Aggregator Latin American 2 Sub 610 A=0.630 G=0.370
Allele Frequency Aggregator Other Sub 478 A=0.699 G=0.301
Allele Frequency Aggregator Latin American 1 Sub 146 A=0.699 G=0.301
Allele Frequency Aggregator Asian Sub 108 A=0.926 G=0.074
Allele Frequency Aggregator South Asian Sub 94 A=0.73 G=0.27
1000Genomes Global Study-wide 5008 A=0.5178 G=0.4822
1000Genomes African Sub 1322 A=0.5189 G=0.4811
1000Genomes East Asian Sub 1008 A=0.5863 G=0.4137
1000Genomes Europe Sub 1006 A=0.4791 G=0.5209
1000Genomes South Asian Sub 978 A=0.514 G=0.486
1000Genomes American Sub 694 A=0.477 G=0.523
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.5799 G=0.4201
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 A=0.667 G=0.333
SGDP_PRJ Global Study-wide 526 A=0.481 G=0.519
Help

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.14930= NC_000001.11:g.14930A>G
GRCh37.p13 chr 1 NC_000001.10:g.14930= NC_000001.10:g.14930A>G
Help

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#.

32 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss5777894 Sep 28, 2016 (149)
2 BCM_SSAHASNP ss9861320 Jul 11, 2003 (116)
3 SC_JCM ss13503859 Dec 05, 2003 (120)
4 CSHL-HAPMAP ss16405344 Feb 28, 2004 (123)
5 SSAHASNP ss35405814 May 24, 2005 (125)
6 BCMHGSC_JDW ss87152753 Mar 25, 2008 (129)
7 HUMANGENOME_JCVI ss95928479 Feb 13, 2009 (131)
8 BGI ss102713365 Dec 01, 2009 (144)
9 ENSEMBL ss131793762 Dec 01, 2009 (144)
10 GMI ss154521897 Dec 01, 2009 (144)
11 BCM-HGSC-SUB ss205165961 Jul 04, 2010 (132)
12 GMI ss275679855 May 04, 2012 (144)
13 GMI ss283987236 Apr 25, 2013 (144)
14 SSMP ss647514739 Apr 25, 2013 (144)
15 1000GENOMES ss1289335481 Aug 21, 2014 (144)
16 DDI ss1425684523 Apr 01, 2015 (144)
17 EVA_MGP ss1710883254 Apr 01, 2015 (144)
18 GENOMED ss1966667259 Jul 19, 2016 (147)
19 GRF ss2697372885 Nov 08, 2017 (151)
20 GNOMAD ss2750601450 Nov 08, 2017 (151)
21 SWEGEN ss2986141334 Nov 08, 2017 (151)
22 TOPMED ss3066316902 Nov 08, 2017 (151)
23 CSHL ss3343271454 Nov 08, 2017 (151)
24 OMUKHERJEE_ADBS ss3646217990 Oct 11, 2018 (152)
25 URBANLAB ss3646580250 Oct 11, 2018 (152)
26 KHV_HUMAN_GENOMES ss3798742405 Jul 12, 2019 (153)
27 SGDP_PRJ ss3847983230 Apr 25, 2020 (154)
28 KRGDB ss3892822913 Apr 25, 2020 (154)
29 FSA-LAB ss3983910136 Apr 25, 2021 (155)
30 FSA-LAB ss3983910137 Apr 25, 2021 (155)
31 EVA ss5141868149 Apr 25, 2021 (155)
32 TOMMO_GENOMICS ss5142031228 Apr 25, 2021 (155)
33 1000Genomes NC_000001.10 - 14930 Oct 11, 2018 (152)
34 KOREAN population from KRGDB NC_000001.10 - 14930 Apr 25, 2020 (154)
35 Medical Genome Project healthy controls from Spanish population NC_000001.10 - 14930 Apr 25, 2020 (154)
36 SGDP_PRJ NC_000001.10 - 14930 Apr 25, 2020 (154)
37 8.3KJPN NC_000001.10 - 14930 Apr 25, 2021 (155)
38 ALFA NC_000001.11 - 14930 Apr 25, 2021 (155)
Help

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)
rs9700845 Feb 27, 2004 (120)
rs11580237 Sep 24, 2004 (123)
rs71268704 Dec 02, 2009 (131)
rs75454623 Jul 01, 2015 (144)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss35405814 NC_000001.8:4792:A:G NC_000001.11:14929:A:G (self)
ss87152753, ss205165961, ss275679855, ss283987236 NC_000001.9:4792:A:G NC_000001.11:14929:A:G (self)
47, 307, 6, 210, 535, ss647514739, ss1289335481, ss1425684523, ss1710883254, ss1966667259, ss2697372885, ss2750601450, ss2986141334, ss3343271454, ss3646217990, ss3847983230, ss3892822913, ss3983910136, ss3983910137, ss5142031228 NC_000001.10:14929:A:G NC_000001.11:14929:A:G (self)
1705841564, ss3066316902, ss3646580250, ss3798742405, ss5141868149 NC_000001.11:14929:A:G NC_000001.11:14929:A:G (self)
ss9861320, ss13503859, ss16405344 NT_077402.1:4792:A:G NC_000001.11:14929:A:G (self)
ss5777894, ss95928479, ss102713365, ss131793762, ss154521897 NT_077402.2:4929:A:G NC_000001.11:14929:A:G (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs6682385

Help

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