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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.

rs2758118

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:15274 (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 / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.2566 (1710/6664, ALFA)
G=0.3472 (1739/5008, 1000G)
T=0.4938 (1425/2886, KOREAN) (+ 1 more)
G=0.228 (127/556, 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.15274A>G
GRCh38.p13 chr 1 NC_000001.11:g.15274A>T
GRCh37.p13 chr 1 NC_000001.10:g.15274A>G
GRCh37.p13 chr 1 NC_000001.10:g.15274A>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
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 6664 A=0.0021 G=0.2566, T=0.7413
European Sub 6534 A=0.0000 G=0.2614, T=0.7386
African Sub 86 A=0.13 G=0.00, T=0.87
African Others Sub 6 A=0.2 G=0.0, T=0.8
African American Sub 80 A=0.12 G=0.00, T=0.88
Asian Sub 4 A=0.0 G=0.0, T=1.0
East Asian Sub 2 A=0.0 G=0.0, T=1.0
Other Asian Sub 2 A=0.0 G=0.0, T=1.0
Latin American 1 Sub 2 A=1.0 G=0.0, T=0.0
Latin American 2 Sub 0 A=0 G=0, T=0
South Asian Sub 4 A=0.0 G=0.0, T=1.0
Other Sub 34 A=0.03 G=0.06, T=0.91


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
1000Genomes Global Study-wide 5008 A=0.0118 G=0.3472, T=0.6410
1000Genomes African Sub 1322 A=0.0401 G=0.3230, T=0.6369
1000Genomes East Asian Sub 1008 A=0.0000 G=0.4812, T=0.5188
1000Genomes Europe Sub 1006 A=0.0000 G=0.2922, T=0.7078
1000Genomes South Asian Sub 978 A=0.003 G=0.350, T=0.647
1000Genomes American Sub 694 A=0.004 G=0.275, T=0.720
KOREAN population from KRGDB KOREAN Study-wide 2886 A=0.0007 G=0.5055, T=0.4938
SGDP_PRJ Global Study-wide 556 A=0.007 G=0.228, T=0.764
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 T
GRCh38.p13 chr 1 NC_000001.11:g.15274= NC_000001.11:g.15274A>G NC_000001.11:g.15274A>T
GRCh37.p13 chr 1 NC_000001.10:g.15274= NC_000001.10:g.15274A>G NC_000001.10:g.15274A>T
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, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss1381151 Oct 08, 2002 (111)
2 TSC-CSHL ss5379723 Oct 08, 2002 (111)
3 SC_JCM ss5932096 Feb 20, 2003 (113)
4 BCMHGSC_JDW ss87152774 Mar 25, 2008 (147)
5 ENSEMBL ss161258212 Dec 01, 2009 (147)
6 GMI ss275679859 May 04, 2012 (147)
7 GMI ss283987237 Apr 25, 2013 (147)
8 BILGI_BIOE ss538305545 Apr 25, 2013 (147)
9 1000GENOMES ss1289335493 Aug 21, 2014 (147)
10 1000GENOMES ss1289335494 Aug 21, 2014 (147)
11 DDI ss1425684527 Apr 01, 2015 (147)
12 GRF ss2697372892 Nov 08, 2017 (151)
13 SWEGEN ss2986141365 Nov 08, 2017 (151)
14 SWEGEN ss2986141366 Nov 08, 2017 (151)
15 TOPMED ss3066317016 Nov 08, 2017 (151)
16 TOPMED ss3066317017 Nov 08, 2017 (151)
17 OMUKHERJEE_ADBS ss3646218003 Oct 11, 2018 (152)
18 URBANLAB ss3646580252 Oct 11, 2018 (152)
19 KHV_HUMAN_GENOMES ss3798742408 Jul 12, 2019 (153)
20 KHV_HUMAN_GENOMES ss3798742409 Jul 12, 2019 (153)
21 SGDP_PRJ ss3847983257 Apr 25, 2020 (154)
22 KRGDB ss3892822950 Apr 25, 2020 (154)
23 GNOMAD ss3986889713 Apr 25, 2021 (155)
24 GNOMAD ss3986889714 Apr 25, 2021 (155)
25 TOMMO_GENOMICS ss5142031286 Apr 25, 2021 (155)
26 TOMMO_GENOMICS ss5142031287 Apr 25, 2021 (155)
27 1000Genomes NC_000001.10 - 15274 Oct 11, 2018 (152)
28 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 1239 (NC_000001.11:15273:A:G 29174/46276)
Row 1240 (NC_000001.11:15273:A:T 12887/42142)

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

Submission ignored due to conflicting rows:
Row 1239 (NC_000001.11:15273:A:G 29174/46276)
Row 1240 (NC_000001.11:15273:A:T 12887/42142)

- Apr 25, 2021 (155)
30 KOREAN population from KRGDB NC_000001.10 - 15274 Apr 25, 2020 (154)
31 SGDP_PRJ NC_000001.10 - 15274 Apr 25, 2020 (154)
32 8.3KJPN

Submission ignored due to conflicting rows:
Row 593 (NC_000001.10:15273:A:G 9268/16744)
Row 594 (NC_000001.10:15273:A:T 7475/16744)

- Apr 25, 2021 (155)
33 8.3KJPN

Submission ignored due to conflicting rows:
Row 593 (NC_000001.10:15273:A:G 9268/16744)
Row 594 (NC_000001.10:15273:A:T 7475/16744)

- Apr 25, 2021 (155)
34 ALFA NC_000001.11 - 15274 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)
rs3871696 Feb 20, 2003 (111)
rs3982631 Dec 16, 2002 (110)
rs4013679 Mar 31, 2003 (113)
rs62636497 Jul 19, 2016 (147)
rs201931625 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
59, 344, 237, ss1289335493, ss2697372892, ss2986141365, ss3847983257, ss3892822950, ss5142031286 NC_000001.10:15273:A:G NC_000001.11:15273:A:G (self)
7627009320, ss3066317016, ss3798742409, ss3986889713 NC_000001.11:15273:A:G NC_000001.11:15273:A:G (self)
ss1381151, ss5379723, ss5932096 NT_077402.3:5273:A:G NC_000001.11:15273:A:G (self)
ss87152774, ss275679859, ss283987237 NC_000001.9:5136:A:T NC_000001.11:15273:A:T (self)
59, 344, 237, ss538305545, ss1289335494, ss1425684527, ss2986141366, ss3646218003, ss3847983257, ss3892822950, ss5142031287 NC_000001.10:15273:A:T NC_000001.11:15273:A:T (self)
77, 7627009320, ss3066317017, ss3646580252, ss3798742408, ss3986889714 NC_000001.11:15273:A:T NC_000001.11:15273:A:T (self)
ss161258212 NT_077402.2:5273:A:T NC_000001.11:15273:A:T (self)
ss5379723, ss5932096 NT_077402.3:5273:A:T NC_000001.11:15273:A: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 rs2758118

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