Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

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.

rs4690

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:14673 (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
G>A / G>C / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.20331 (3407/16758, 8.3KJPN)
C=0.10861 (1758/16186, ALFA)
C=0.1691 (494/2922, KOREAN) (+ 2 more)
G=0.500 (137/274, SGDP_PRJ)
C=0.500 (137/274, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
WASH7P : Non Coding Transcript Variant
DDX11L1 : 500B Downstream 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.14673G>A
GRCh38.p13 chr 1 NC_000001.11:g.14673G>C
GRCh38.p13 chr 1 NC_000001.11:g.14673G>T
GRCh37.p13 chr 1 NC_000001.10:g.14673G>A
GRCh37.p13 chr 1 NC_000001.10:g.14673G>C
GRCh37.p13 chr 1 NC_000001.10:g.14673G>T
Gene: WASH7P, WASP family homolog 7, pseudogene (minus strand)
Molecule type Change Amino acid[Codon] SO Term
WASH7P transcript NR_024540.1:n.1458C>T N/A Non Coding Transcript Variant
WASH7P transcript NR_024540.1:n.1458C>G N/A Non Coding Transcript Variant
WASH7P transcript NR_024540.1:n.1458C>A N/A Non Coding Transcript Variant
Gene: DDX11L1, DEAD/H-box helicase 11 like 1 (pseudogene) (plus strand) : 500B Downstream Variant
Molecule type Change Amino acid[Codon] SO Term
DDX11L1 transcript NR_046018.2:n. N/A Downstream Transcript 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 (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 16186 G=0.89139 A=0.00000, C=0.10861, T=0.00000
European Sub 12010 G=0.85396 A=0.00000, C=0.14604, T=0.00000
African Sub 2744 G=1.0000 A=0.0000, C=0.0000, T=0.0000
African Others Sub 104 G=1.000 A=0.000, C=0.000, T=0.000
African American Sub 2640 G=1.0000 A=0.0000, C=0.0000, T=0.0000
Asian Sub 108 G=1.000 A=0.000, C=0.000, T=0.000
East Asian Sub 84 G=1.00 A=0.00, C=0.00, T=0.00
Other Asian Sub 24 G=1.00 A=0.00, C=0.00, T=0.00
Latin American 1 Sub 144 G=1.000 A=0.000, C=0.000, T=0.000
Latin American 2 Sub 608 G=1.000 A=0.000, C=0.000, T=0.000
South Asian Sub 94 G=1.00 A=0.00, C=0.00, T=0.00
Other Sub 478 G=0.992 A=0.000, C=0.008, T=0.000


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 16758 G=0.79669 C=0.20331
KOREAN population from KRGDB KOREAN Study-wide 2922 G=0.8309 C=0.1691
SGDP_PRJ Global Study-wide 274 G=0.500 C=0.500
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 G= A C T
GRCh38.p13 chr 1 NC_000001.11:g.14673= NC_000001.11:g.14673G>A NC_000001.11:g.14673G>C NC_000001.11:g.14673G>T
GRCh37.p13 chr 1 NC_000001.10:g.14673= NC_000001.10:g.14673G>A NC_000001.10:g.14673G>C NC_000001.10:g.14673G>T
WASH7P transcript NR_024540.1:n.1458= NR_024540.1:n.1458C>T NR_024540.1:n.1458C>G NR_024540.1:n.1458C>A
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#.

26 SubSNP, 7 Frequency submissions
No Submitter Submission ID Date (Build)
1 UWGC ss7378 Sep 19, 2000 (52)
2 CGAP-GAI ss11188 Sep 19, 2000 (52)
3 TSC-CSHL ss5379714 Oct 10, 2002 (113)
4 SC_JCM ss5859137 Sep 28, 2016 (149)
5 BCM_SSAHASNP ss9885333 Sep 28, 2016 (149)
6 SC_JCM ss11206021 Sep 28, 2016 (149)
7 CSHL-HAPMAP ss16414892 Sep 28, 2016 (149)
8 SSAHASNP ss35239368 May 24, 2005 (144)
9 HUMANGENOME_JCVI ss95842117 Feb 13, 2009 (144)
10 ENSEMBL ss136948429 Dec 01, 2009 (144)
11 ENSEMBL ss139722228 Dec 01, 2009 (144)
12 GMI ss156963037 Dec 01, 2009 (144)
13 SSMP ss647514735 Apr 25, 2013 (144)
14 PADH-LAB_SPU ss1751134591 Sep 08, 2015 (146)
15 SWEGEN ss2986141318 Nov 08, 2017 (151)
16 TOPMED ss3066316811 Nov 08, 2017 (151)
17 TOPMED ss3066316812 Nov 08, 2017 (151)
18 TOPMED ss3066316813 Nov 08, 2017 (151)
19 OMUKHERJEE_ADBS ss3646217978 Oct 11, 2018 (152)
20 URBANLAB ss3646580248 Oct 11, 2018 (152)
21 SGDP_PRJ ss3847983217 Apr 25, 2020 (154)
22 KRGDB ss3892822891 Apr 25, 2020 (154)
23 GNOMAD ss3986889645 Apr 25, 2021 (155)
24 GNOMAD ss3986889646 Apr 25, 2021 (155)
25 GNOMAD ss3986889647 Apr 25, 2021 (155)
26 TOMMO_GENOMICS ss5142031186 Apr 25, 2021 (155)
27 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 1056 (NC_000001.11:14672:G:A 117/130010)
Row 1057 (NC_000001.11:14672:G:C 402/129586)
Row 1058 (NC_000001.11:14672:G:T 12/130112)

- Apr 25, 2021 (155)
28 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 1056 (NC_000001.11:14672:G:A 117/130010)
Row 1057 (NC_000001.11:14672:G:C 402/129586)
Row 1058 (NC_000001.11:14672:G:T 12/130112)

- Apr 25, 2021 (155)
29 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 1056 (NC_000001.11:14672:G:A 117/130010)
Row 1057 (NC_000001.11:14672:G:C 402/129586)
Row 1058 (NC_000001.11:14672:G:T 12/130112)

- Apr 25, 2021 (155)
30 KOREAN population from KRGDB NC_000001.10 - 14673 Apr 25, 2020 (154)
31 SGDP_PRJ NC_000001.10 - 14673 Apr 25, 2020 (154)
32 8.3KJPN NC_000001.10 - 14673 Apr 25, 2021 (155)
33 ALFA NC_000001.11 - 14673 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)
rs2376562 Aug 27, 2003 (117)
rs3185571 Jul 03, 2002 (106)
rs3982627 Dec 16, 2002 (110)
rs4021646 Feb 20, 2003 (111)
rs4030210 Mar 31, 2003 (113)
rs6600760 Apr 05, 2004 (121)
rs11582131 Apr 09, 2015 (144)
rs71252254 Dec 02, 2009 (131)
rs78384070 Jul 04, 2010 (132)
rs369473859 Jul 01, 2015 (144)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
6640926379, ss3066316811, ss3986889645 NC_000001.11:14672:G:A NC_000001.11:14672:G:A (self)
ss35239368 NC_000001.8:4535:G:C NC_000001.11:14672:G:C (self)
285, 197, 493, ss647514735, ss1751134591, ss2986141318, ss3646217978, ss3847983217, ss3892822891, ss5142031186 NC_000001.10:14672:G:C NC_000001.11:14672:G:C (self)
6640926379, ss3066316812, ss3646580248, ss3986889646 NC_000001.11:14672:G:C NC_000001.11:14672:G:C (self)
ss9885333, ss11206021, ss16414892 NT_077402.1:4535:G:C NC_000001.11:14672:G:C (self)
ss7378, ss11188, ss5379714, ss5859137, ss95842117, ss136948429, ss139722228, ss156963037 NT_077402.2:4672:G:C NC_000001.11:14672:G:C (self)
6640926379, ss3066316813, ss3986889647 NC_000001.11:14672:G:T NC_000001.11:14672:G:T (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 rs4690

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