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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.

rs878915777

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:14773 (GRCh38.p14) 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
C>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.00021 (6/28258, 14KJPN)
T=0.00066 (11/16760, 8.3KJPN)
T=0.00846 (136/16076, ALFA) (+ 4 more)
T=0.0084 (54/6404, 1000G_30x)
T=0.0007 (2/2920, KOREAN)
C=0.5 (4/8, SGDP_PRJ)
T=0.5 (4/8, 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

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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 16076 C=0.99154 G=0.00000, T=0.00846
European Sub 11876 C=0.98905 G=0.00000, T=0.01095
African Sub 2790 C=0.9978 G=0.0000, T=0.0022
African Others Sub 108 C=0.991 G=0.000, T=0.009
African American Sub 2682 C=0.9981 G=0.0000, T=0.0019
Asian Sub 108 C=1.000 G=0.000, T=0.000
East Asian Sub 84 C=1.00 G=0.00, T=0.00
Other Asian Sub 24 C=1.00 G=0.00, T=0.00
Latin American 1 Sub 144 C=1.000 G=0.000, T=0.000
Latin American 2 Sub 604 C=1.000 G=0.000, T=0.000
South Asian Sub 90 C=1.00 G=0.00, T=0.00
Other Sub 464 C=1.000 G=0.000, 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
14KJPN JAPANESE Study-wide 28258 C=0.99979 T=0.00021
8.3KJPN JAPANESE Study-wide 16760 C=0.99934 T=0.00066
Allele Frequency Aggregator Total Global 16076 C=0.99154 G=0.00000, T=0.00846
Allele Frequency Aggregator European Sub 11876 C=0.98905 G=0.00000, T=0.01095
Allele Frequency Aggregator African Sub 2790 C=0.9978 G=0.0000, T=0.0022
Allele Frequency Aggregator Latin American 2 Sub 604 C=1.000 G=0.000, T=0.000
Allele Frequency Aggregator Other Sub 464 C=1.000 G=0.000, T=0.000
Allele Frequency Aggregator Latin American 1 Sub 144 C=1.000 G=0.000, T=0.000
Allele Frequency Aggregator Asian Sub 108 C=1.000 G=0.000, T=0.000
Allele Frequency Aggregator South Asian Sub 90 C=1.00 G=0.00, T=0.00
1000Genomes_30x Global Study-wide 6404 C=0.9916 T=0.0084
1000Genomes_30x African Sub 1786 C=0.9927 T=0.0073
1000Genomes_30x Europe Sub 1266 C=0.9850 T=0.0150
1000Genomes_30x South Asian Sub 1202 C=0.9850 T=0.0150
1000Genomes_30x East Asian Sub 1170 C=0.9991 T=0.0009
1000Genomes_30x American Sub 980 C=0.997 T=0.003
KOREAN population from KRGDB KOREAN Study-wide 2920 C=0.9993 T=0.0007
SGDP_PRJ Global Study-wide 8 C=0.5 T=0.5
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.p14 chr 1 NC_000001.11:g.14773C>G
GRCh38.p14 chr 1 NC_000001.11:g.14773C>T
GRCh37.p13 chr 1 NC_000001.10:g.14773C>G
GRCh37.p13 chr 1 NC_000001.10:g.14773C>T
Gene: WASH7P, WASP family homolog 7, pseudogene (minus strand)
Molecule type Change Amino acid[Codon] SO Term
WASH7P transcript NR_024540.1:n.1358G>C N/A Non Coding Transcript Variant
WASH7P transcript NR_024540.1:n.1358G>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
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 C= G T
GRCh38.p14 chr 1 NC_000001.11:g.14773= NC_000001.11:g.14773C>G NC_000001.11:g.14773C>T
GRCh37.p13 chr 1 NC_000001.10:g.14773= NC_000001.10:g.14773C>G NC_000001.10:g.14773C>T
WASH7P transcript NR_024540.1:n.1358= NR_024540.1:n.1358G>C NR_024540.1:n.1358G>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#.

13 SubSNP, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 TMC_SNPDB ss1997003400 Jul 19, 2016 (147)
2 GNOMAD ss2750601412 Nov 08, 2017 (151)
3 SWEGEN ss2986141323 Nov 08, 2017 (151)
4 CSHL ss3343271452 Nov 08, 2017 (151)
5 OMUKHERJEE_ADBS ss3646217984 Oct 11, 2018 (152)
6 SGDP_PRJ ss3847983225 Apr 25, 2020 (154)
7 KRGDB ss3892822901 Apr 25, 2020 (154)
8 TOMMO_GENOMICS ss5142031203 Apr 25, 2021 (155)
9 1000G_HIGH_COVERAGE ss5240854599 Oct 12, 2022 (156)
10 EVA ss5316170632 Oct 12, 2022 (156)
11 1000G_HIGH_COVERAGE ss5512474206 Oct 12, 2022 (156)
12 SANFORD_IMAGENETICS ss5624742000 Oct 12, 2022 (156)
13 TOMMO_GENOMICS ss5666163557 Oct 12, 2022 (156)
14 1000Genomes_30x NC_000001.11 - 14773 Oct 12, 2022 (156)
15 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 1091 (NC_000001.11:14772:C:G 1/136708)
Row 1092 (NC_000001.11:14772:C:T 1582/135978)

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

Submission ignored due to conflicting rows:
Row 1091 (NC_000001.11:14772:C:G 1/136708)
Row 1092 (NC_000001.11:14772:C:T 1582/135978)

- Apr 25, 2021 (155)
17 KOREAN population from KRGDB NC_000001.10 - 14773 Apr 25, 2020 (154)
18 SGDP_PRJ NC_000001.10 - 14773 Apr 25, 2020 (154)
19 8.3KJPN NC_000001.10 - 14773 Apr 25, 2021 (155)
20 14KJPN NC_000001.11 - 14773 Oct 12, 2022 (156)
21 ALFA NC_000001.11 - 14773 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
8876032828 NC_000001.11:14772:C:G NC_000001.11:14772:C:G (self)
295, 205, 510, ss1997003400, ss2750601412, ss2986141323, ss3343271452, ss3646217984, ss3847983225, ss3892822901, ss5142031203, ss5316170632, ss5624742000 NC_000001.10:14772:C:T NC_000001.11:14772:C:T (self)
141, 661, 8876032828, ss5240854599, ss5512474206, ss5666163557 NC_000001.11:14772:C:T NC_000001.11:14772:C: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 rs878915777

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.post761+d5e8e07