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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs1476459674

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr12:108232895 (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
G>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.000004 (1/264690, TOPMED)
C=0.00008 (1/11862, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
WSCD2 : Missense Variant
LOC124903077 : Intron 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: 20231103111315
Population Group Sample Size Ref Allele Alt Allele Ref HMOZ Alt HMOZ HTRZ HWEP
Total Global 11862 G=0.99992 C=0.00008 0.999831 0.0 0.000169 0
European Sub 7618 G=1.0000 C=0.0000 1.0 0.0 0.0 N/A
African Sub 2816 G=0.9996 C=0.0004 0.99929 0.0 0.00071 0
African Others Sub 108 G=1.000 C=0.000 1.0 0.0 0.0 N/A
African American Sub 2708 G=0.9996 C=0.0004 0.999261 0.0 0.000739 0
Asian Sub 108 G=1.000 C=0.000 1.0 0.0 0.0 N/A
East Asian Sub 84 G=1.00 C=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 24 G=1.00 C=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 G=1.000 C=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 G=1.000 C=0.000 1.0 0.0 0.0 N/A
South Asian Sub 94 G=1.00 C=0.00 1.0 0.0 0.0 N/A
Other Sub 470 G=1.000 C=0.000 1.0 0.0 0.0 N/A


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
TopMed Global Study-wide 264690 G=0.999996 C=0.000004
Allele Frequency Aggregator Total Global 11862 G=0.99992 C=0.00008
Allele Frequency Aggregator European Sub 7618 G=1.0000 C=0.0000
Allele Frequency Aggregator African Sub 2816 G=0.9996 C=0.0004
Allele Frequency Aggregator Latin American 2 Sub 610 G=1.000 C=0.000
Allele Frequency Aggregator Other Sub 470 G=1.000 C=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 G=1.000 C=0.000
Allele Frequency Aggregator Asian Sub 108 G=1.000 C=0.000
Allele Frequency Aggregator South Asian Sub 94 G=1.00 C=0.00
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 12 NC_000012.12:g.108232895G>C
GRCh37.p13 chr 12 NC_000012.11:g.108626672G>C
Gene: WSCD2, WSC domain containing 2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
WSCD2 transcript variant 1 NM_014653.4:c.1144G>C G [GGG] > R [CGG] Coding Sequence Variant
sialate:O-sulfotransferase 2 NP_055468.2:p.Gly382Arg G (Gly) > R (Arg) Missense Variant
WSCD2 transcript variant 2 NM_001304447.2:c.1144G>C G [GGG] > R [CGG] Coding Sequence Variant
sialate:O-sulfotransferase 2 NP_001291376.1:p.Gly382Arg G (Gly) > R (Arg) Missense Variant
WSCD2 transcript variant X1 XM_017020243.2:c.1144G>C G [GGG] > R [CGG] Coding Sequence Variant
sialate:O-sulfotransferase 2 isoform X1 XP_016875732.1:p.Gly382Arg G (Gly) > R (Arg) Missense Variant
WSCD2 transcript variant X2 XM_017020244.2:c.1144G>C G [GGG] > R [CGG] Coding Sequence Variant
sialate:O-sulfotransferase 2 isoform X1 XP_016875733.1:p.Gly382Arg G (Gly) > R (Arg) Missense Variant
WSCD2 transcript variant X3 XM_017020245.2:c.1144G>C G [GGG] > R [CGG] Coding Sequence Variant
sialate:O-sulfotransferase 2 isoform X1 XP_016875734.1:p.Gly382Arg G (Gly) > R (Arg) Missense Variant
WSCD2 transcript variant X4 XM_017020246.3:c.1144G>C G [GGG] > R [CGG] Coding Sequence Variant
sialate:O-sulfotransferase 2 isoform X1 XP_016875735.1:p.Gly382Arg G (Gly) > R (Arg) Missense Variant
WSCD2 transcript variant X5 XM_017020247.2:c.1144G>C G [GGG] > R [CGG] Coding Sequence Variant
sialate:O-sulfotransferase 2 isoform X1 XP_016875736.1:p.Gly382Arg G (Gly) > R (Arg) Missense Variant
WSCD2 transcript variant X6 XM_017020248.2:c.1144G>C G [GGG] > R [CGG] Coding Sequence Variant
sialate:O-sulfotransferase 2 isoform X1 XP_016875737.1:p.Gly382Arg G (Gly) > R (Arg) Missense Variant
WSCD2 transcript variant X7 XM_017020250.3:c.844G>C G [GGG] > R [CGG] Coding Sequence Variant
sialate:O-sulfotransferase 2 isoform X2 XP_016875739.1:p.Gly282Arg G (Gly) > R (Arg) Missense Variant
WSCD2 transcript variant X8 XM_017020251.3:c.844G>C G [GGG] > R [CGG] Coding Sequence Variant
sialate:O-sulfotransferase 2 isoform X2 XP_016875740.1:p.Gly282Arg G (Gly) > R (Arg) Missense Variant
WSCD2 transcript variant X9 XM_047429913.1:c.844G>C G [GGG] > R [CGG] Coding Sequence Variant
sialate:O-sulfotransferase 2 isoform X2 XP_047285869.1:p.Gly282Arg G (Gly) > R (Arg) Missense Variant
WSCD2 transcript variant X10 XM_017020252.2:c.844G>C G [GGG] > R [CGG] Coding Sequence Variant
sialate:O-sulfotransferase 2 isoform X2 XP_016875741.1:p.Gly282Arg G (Gly) > R (Arg) Missense Variant
WSCD2 transcript variant X11 XM_047429914.1:c.1144G>C G [GGG] > R [CGG] Coding Sequence Variant
sialate:O-sulfotransferase 2 isoform X3 XP_047285870.1:p.Gly382Arg G (Gly) > R (Arg) Missense Variant
Gene: LOC124903077, uncharacterized LOC124903077 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC124903077 transcript variant X1 XR_007063583.1:n. N/A Intron Variant
LOC124903077 transcript variant X2 XR_007063584.1: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
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= C
GRCh38.p14 chr 12 NC_000012.12:g.108232895= NC_000012.12:g.108232895G>C
GRCh37.p13 chr 12 NC_000012.11:g.108626672= NC_000012.11:g.108626672G>C
WSCD2 transcript variant 1 NM_014653.4:c.1144= NM_014653.4:c.1144G>C
WSCD2 transcript variant 1 NM_014653.3:c.1144= NM_014653.3:c.1144G>C
WSCD2 transcript NM_014653.2:c.1144= NM_014653.2:c.1144G>C
WSCD2 transcript variant X7 XM_017020250.3:c.844= XM_017020250.3:c.844G>C
WSCD2 transcript variant X8 XM_017020250.2:c.844= XM_017020250.2:c.844G>C
WSCD2 transcript variant X8 XM_017020250.1:c.844= XM_017020250.1:c.844G>C
WSCD2 transcript variant X4 XM_017020246.3:c.1144= XM_017020246.3:c.1144G>C
WSCD2 transcript variant X4 XM_017020246.2:c.1144= XM_017020246.2:c.1144G>C
WSCD2 transcript variant X4 XM_017020246.1:c.1144= XM_017020246.1:c.1144G>C
WSCD2 transcript variant X8 XM_017020251.3:c.844= XM_017020251.3:c.844G>C
WSCD2 transcript variant X9 XM_017020251.2:c.844= XM_017020251.2:c.844G>C
WSCD2 transcript variant X9 XM_017020251.1:c.844= XM_017020251.1:c.844G>C
WSCD2 transcript variant X2 XM_017020244.2:c.1144= XM_017020244.2:c.1144G>C
WSCD2 transcript variant X2 XM_017020244.1:c.1144= XM_017020244.1:c.1144G>C
WSCD2 transcript variant X6 XM_017020248.2:c.1144= XM_017020248.2:c.1144G>C
WSCD2 transcript variant X6 XM_017020248.1:c.1144= XM_017020248.1:c.1144G>C
WSCD2 transcript variant X1 XM_017020243.2:c.1144= XM_017020243.2:c.1144G>C
WSCD2 transcript variant X1 XM_017020243.1:c.1144= XM_017020243.1:c.1144G>C
WSCD2 transcript variant X10 XM_017020252.2:c.844= XM_017020252.2:c.844G>C
WSCD2 transcript variant X10 XM_017020252.1:c.844= XM_017020252.1:c.844G>C
WSCD2 transcript variant X3 XM_017020245.2:c.1144= XM_017020245.2:c.1144G>C
WSCD2 transcript variant X3 XM_017020245.1:c.1144= XM_017020245.1:c.1144G>C
WSCD2 transcript variant X5 XM_017020247.2:c.1144= XM_017020247.2:c.1144G>C
WSCD2 transcript variant X5 XM_017020247.1:c.1144= XM_017020247.1:c.1144G>C
WSCD2 transcript variant 2 NM_001304447.2:c.1144= NM_001304447.2:c.1144G>C
WSCD2 transcript variant 2 NM_001304447.1:c.1144= NM_001304447.1:c.1144G>C
WSCD2 transcript variant X9 XM_047429913.1:c.844= XM_047429913.1:c.844G>C
WSCD2 transcript variant X11 XM_047429914.1:c.1144= XM_047429914.1:c.1144G>C
sialate:O-sulfotransferase 2 NP_055468.2:p.Gly382= NP_055468.2:p.Gly382Arg
sialate:O-sulfotransferase 2 isoform X2 XP_016875739.1:p.Gly282= XP_016875739.1:p.Gly282Arg
sialate:O-sulfotransferase 2 isoform X1 XP_016875735.1:p.Gly382= XP_016875735.1:p.Gly382Arg
sialate:O-sulfotransferase 2 isoform X2 XP_016875740.1:p.Gly282= XP_016875740.1:p.Gly282Arg
sialate:O-sulfotransferase 2 isoform X1 XP_016875733.1:p.Gly382= XP_016875733.1:p.Gly382Arg
sialate:O-sulfotransferase 2 isoform X1 XP_016875737.1:p.Gly382= XP_016875737.1:p.Gly382Arg
sialate:O-sulfotransferase 2 isoform X1 XP_016875732.1:p.Gly382= XP_016875732.1:p.Gly382Arg
sialate:O-sulfotransferase 2 isoform X2 XP_016875741.1:p.Gly282= XP_016875741.1:p.Gly282Arg
sialate:O-sulfotransferase 2 isoform X1 XP_016875734.1:p.Gly382= XP_016875734.1:p.Gly382Arg
sialate:O-sulfotransferase 2 isoform X1 XP_016875736.1:p.Gly382= XP_016875736.1:p.Gly382Arg
sialate:O-sulfotransferase 2 NP_001291376.1:p.Gly382= NP_001291376.1:p.Gly382Arg
sialate:O-sulfotransferase 2 isoform X2 XP_047285869.1:p.Gly282= XP_047285869.1:p.Gly282Arg
sialate:O-sulfotransferase 2 isoform X3 XP_047285870.1:p.Gly382= XP_047285870.1:p.Gly382Arg
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#.

1 SubSNP, 2 Frequency submissions
No Submitter Submission ID Date (Build)
1 TOPMED ss4932137246 Apr 26, 2021 (155)
2 TopMed NC_000012.12 - 108232895 Apr 26, 2021 (155)
3 ALFA NC_000012.12 - 108232895 Apr 26, 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
147682903, 12451605187, ss4932137246 NC_000012.12:108232894:G:C NC_000012.12:108232894:G:C (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 rs1476459674

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.post820+afb47a3d