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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.

rs1476802388

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:153618918 (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>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000007 (1/140234, GnomAD)
A=0.00000 (0/10680, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
S100A13 : Missense 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 10680 C=1.00000 A=0.00000 1.0 0.0 0.0 N/A
European Sub 6962 C=1.0000 A=0.0000 1.0 0.0 0.0 N/A
African Sub 2294 C=1.0000 A=0.0000 1.0 0.0 0.0 N/A
African Others Sub 84 C=1.00 A=0.00 1.0 0.0 0.0 N/A
African American Sub 2210 C=1.0000 A=0.0000 1.0 0.0 0.0 N/A
Asian Sub 108 C=1.000 A=0.000 1.0 0.0 0.0 N/A
East Asian Sub 84 C=1.00 A=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 24 C=1.00 A=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 C=1.000 A=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 C=1.000 A=0.000 1.0 0.0 0.0 N/A
South Asian Sub 94 C=1.00 A=0.00 1.0 0.0 0.0 N/A
Other Sub 466 C=1.000 A=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
gnomAD - Genomes Global Study-wide 140234 C=0.999993 A=0.000007
gnomAD - Genomes European Sub 75942 C=1.00000 A=0.00000
gnomAD - Genomes African Sub 42018 C=0.99998 A=0.00002
gnomAD - Genomes American Sub 13668 C=1.00000 A=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3324 C=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3132 C=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2150 C=1.0000 A=0.0000
Allele Frequency Aggregator Total Global 10680 C=1.00000 A=0.00000
Allele Frequency Aggregator European Sub 6962 C=1.0000 A=0.0000
Allele Frequency Aggregator African Sub 2294 C=1.0000 A=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 C=1.000 A=0.000
Allele Frequency Aggregator Other Sub 466 C=1.000 A=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 C=1.000 A=0.000
Allele Frequency Aggregator Asian Sub 108 C=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 94 C=1.00 A=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 1 NC_000001.11:g.153618918C>A
GRCh37.p13 chr 1 NC_000001.10:g.153591394C>A
Gene: S100A13, S100 calcium binding protein A13 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
S100A13 transcript variant 1 NM_001024210.2:c.274G>T D [GAC] > Y [TAC] Coding Sequence Variant
protein S100-A13 NP_001019381.1:p.Asp92Tyr D (Asp) > Y (Tyr) Missense Variant
S100A13 transcript variant 4 NM_001024212.2:c.274G>T D [GAC] > Y [TAC] Coding Sequence Variant
protein S100-A13 NP_001019383.1:p.Asp92Tyr D (Asp) > Y (Tyr) Missense Variant
S100A13 transcript variant 5 NM_001024213.2:c.274G>T D [GAC] > Y [TAC] Coding Sequence Variant
protein S100-A13 NP_001019384.1:p.Asp92Tyr D (Asp) > Y (Tyr) Missense Variant
S100A13 transcript variant 3 NM_001024211.2:c.274G>T D [GAC] > Y [TAC] Coding Sequence Variant
protein S100-A13 NP_001019382.1:p.Asp92Tyr D (Asp) > Y (Tyr) Missense Variant
S100A13 transcript variant 2 NM_005979.3:c.274G>T D [GAC] > Y [TAC] Coding Sequence Variant
protein S100-A13 NP_005970.1:p.Asp92Tyr D (Asp) > Y (Tyr) Missense Variant
S100A13 transcript variant X1 XM_047427400.1:c. N/A Genic Downstream Transcript Variant
S100A13 transcript variant X2 XM_047427401.1:c.274G>T D [GAC] > Y [TAC] Coding Sequence Variant
protein S100-A13 isoform X2 XP_047283357.1:p.Asp92Tyr D (Asp) > Y (Tyr) Missense Variant
S100A13 transcript variant X3 XM_011509862.4:c.274G>T D [GAC] > Y [TAC] Coding Sequence Variant
protein S100-A13 isoform X2 XP_011508164.1:p.Asp92Tyr D (Asp) > Y (Tyr) Missense Variant
S100A13 transcript variant X4 XM_005245434.4:c.274G>T D [GAC] > Y [TAC] Coding Sequence Variant
protein S100-A13 isoform X2 XP_005245491.1:p.Asp92Tyr D (Asp) > Y (Tyr) Missense Variant
S100A13 transcript variant X5 XM_047427404.1:c.274G>T D [GAC] > Y [TAC] Coding Sequence Variant
protein S100-A13 isoform X2 XP_047283360.1:p.Asp92Tyr D (Asp) > Y (Tyr) Missense Variant
S100A13 transcript variant X6 XM_017002034.3:c.274G>T D [GAC] > Y [TAC] Coding Sequence Variant
protein S100-A13 isoform X2 XP_016857523.1:p.Asp92Tyr D (Asp) > Y (Tyr) Missense Variant
S100A13 transcript variant X7 XM_047427406.1:c.274G>T D [GAC] > Y [TAC] Coding Sequence Variant
protein S100-A13 isoform X2 XP_047283362.1:p.Asp92Tyr D (Asp) > Y (Tyr) Missense Variant
S100A13 transcript variant X8 XM_047427407.1:c.274G>T D [GAC] > Y [TAC] Coding Sequence Variant
protein S100-A13 isoform X2 XP_047283363.1:p.Asp92Tyr D (Asp) > Y (Tyr) Missense Variant
S100A13 transcript variant X9 XM_047427408.1:c.274G>T D [GAC] > Y [TAC] Coding Sequence Variant
protein S100-A13 isoform X2 XP_047283364.1:p.Asp92Tyr D (Asp) > Y (Tyr) Missense Variant
S100A13 transcript variant X10 XM_047427409.1:c.274G>T D [GAC] > Y [TAC] Coding Sequence Variant
protein S100-A13 isoform X2 XP_047283365.1:p.Asp92Tyr D (Asp) > Y (Tyr) Missense Variant
S100A13 transcript variant X11 XM_017002035.3:c.274G>T D [GAC] > Y [TAC] Coding Sequence Variant
protein S100-A13 isoform X2 XP_016857524.1:p.Asp92Tyr D (Asp) > Y (Tyr) Missense Variant
S100A13 transcript variant X12 XM_047427410.1:c.274G>T D [GAC] > Y [TAC] Coding Sequence Variant
protein S100-A13 isoform X2 XP_047283366.1:p.Asp92Tyr D (Asp) > Y (Tyr) Missense Variant
S100A13 transcript variant X13 XM_047427413.1:c.274G>T D [GAC] > Y [TAC] Coding Sequence Variant
protein S100-A13 isoform X2 XP_047283369.1:p.Asp92Tyr D (Asp) > Y (Tyr) Missense Variant
S100A13 transcript variant X14 XM_047427417.1:c.274G>T D [GAC] > Y [TAC] Coding Sequence Variant
protein S100-A13 isoform X2 XP_047283373.1:p.Asp92Tyr D (Asp) > Y (Tyr) Missense Variant
S100A13 transcript variant X15 XM_047427419.1:c.274G>T D [GAC] > Y [TAC] Coding Sequence Variant
protein S100-A13 isoform X2 XP_047283375.1:p.Asp92Tyr D (Asp) > Y (Tyr) Missense Variant
S100A13 transcript variant X16 XM_017002036.2:c.274G>T D [GAC] > Y [TAC] Coding Sequence Variant
protein S100-A13 isoform X2 XP_016857525.1:p.Asp92Tyr D (Asp) > Y (Tyr) Missense Variant
S100A13 transcript variant X17 XM_047427433.1:c.274G>T D [GAC] > Y [TAC] Coding Sequence Variant
protein S100-A13 isoform X2 XP_047283389.1:p.Asp92Tyr D (Asp) > Y (Tyr) Missense Variant
S100A13 transcript variant X18 XM_047427435.1:c.274G>T D [GAC] > Y [TAC] Coding Sequence Variant
protein S100-A13 isoform X2 XP_047283391.1:p.Asp92Tyr D (Asp) > Y (Tyr) Missense Variant
S100A13 transcript variant X19 XM_047427439.1:c.274G>T D [GAC] > Y [TAC] Coding Sequence Variant
protein S100-A13 isoform X2 XP_047283395.1:p.Asp92Tyr D (Asp) > Y (Tyr) Missense Variant
S100A13 transcript variant X20 XM_047427444.1:c.274G>T D [GAC] > Y [TAC] Coding Sequence Variant
protein S100-A13 isoform X2 XP_047283400.1:p.Asp92Tyr D (Asp) > Y (Tyr) Missense Variant
S100A13 transcript variant X21 XM_047427445.1:c.274G>T D [GAC] > Y [TAC] Coding Sequence Variant
protein S100-A13 isoform X2 XP_047283401.1:p.Asp92Tyr D (Asp) > Y (Tyr) Missense Variant
S100A13 transcript variant X22 XM_047427446.1:c.274G>T D [GAC] > Y [TAC] Coding Sequence Variant
protein S100-A13 isoform X2 XP_047283402.1:p.Asp92Tyr D (Asp) > Y (Tyr) Missense 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= A
GRCh38.p14 chr 1 NC_000001.11:g.153618918= NC_000001.11:g.153618918C>A
GRCh37.p13 chr 1 NC_000001.10:g.153591394= NC_000001.10:g.153591394C>A
S100A13 transcript variant X3 XM_011509862.4:c.274= XM_011509862.4:c.274G>T
S100A13 transcript variant X1 XM_011509862.3:c.274= XM_011509862.3:c.274G>T
S100A13 transcript variant X1 XM_011509862.2:c.274= XM_011509862.2:c.274G>T
S100A13 transcript variant X1 XM_011509862.1:c.274= XM_011509862.1:c.274G>T
S100A13 transcript variant X4 XM_005245434.4:c.274= XM_005245434.4:c.274G>T
S100A13 transcript variant X4 XM_005245434.3:c.274= XM_005245434.3:c.274G>T
S100A13 transcript variant X2 XM_005245434.2:c.274= XM_005245434.2:c.274G>T
S100A13 transcript variant X2 XM_005245434.1:c.274= XM_005245434.1:c.274G>T
S100A13 transcript variant X11 XM_017002035.3:c.274= XM_017002035.3:c.274G>T
S100A13 transcript variant X6 XM_017002035.2:c.274= XM_017002035.2:c.274G>T
S100A13 transcript variant X6 XM_017002035.1:c.274= XM_017002035.1:c.274G>T
S100A13 transcript variant X6 XM_017002034.3:c.274= XM_017002034.3:c.274G>T
S100A13 transcript variant X3 XM_017002034.2:c.274= XM_017002034.2:c.274G>T
S100A13 transcript variant X3 XM_017002034.1:c.274= XM_017002034.1:c.274G>T
S100A13 transcript variant 2 NM_005979.3:c.274= NM_005979.3:c.274G>T
S100A13 transcript variant 2 NM_005979.2:c.274= NM_005979.2:c.274G>T
S100A13 transcript variant 1 NM_001024210.2:c.274= NM_001024210.2:c.274G>T
S100A13 transcript variant 1 NM_001024210.1:c.274= NM_001024210.1:c.274G>T
S100A13 transcript variant 5 NM_001024213.2:c.274= NM_001024213.2:c.274G>T
S100A13 transcript variant 5 NM_001024213.1:c.274= NM_001024213.1:c.274G>T
S100A13 transcript variant X16 XM_017002036.2:c.274= XM_017002036.2:c.274G>T
S100A13 transcript variant X7 XM_017002036.1:c.274= XM_017002036.1:c.274G>T
S100A13 transcript variant 4 NM_001024212.2:c.274= NM_001024212.2:c.274G>T
S100A13 transcript variant 4 NM_001024212.1:c.274= NM_001024212.1:c.274G>T
S100A13 transcript variant 3 NM_001024211.2:c.274= NM_001024211.2:c.274G>T
S100A13 transcript variant 3 NM_001024211.1:c.274= NM_001024211.1:c.274G>T
S100A13 transcript variant X10 XM_047427409.1:c.274= XM_047427409.1:c.274G>T
S100A13 transcript variant X2 XM_047427401.1:c.274= XM_047427401.1:c.274G>T
S100A13 transcript variant X19 XM_047427439.1:c.274= XM_047427439.1:c.274G>T
S100A13 transcript variant X20 XM_047427444.1:c.274= XM_047427444.1:c.274G>T
S100A13 transcript variant X21 XM_047427445.1:c.274= XM_047427445.1:c.274G>T
S100A13 transcript variant X8 XM_047427407.1:c.274= XM_047427407.1:c.274G>T
S100A13 transcript variant X9 XM_047427408.1:c.274= XM_047427408.1:c.274G>T
S100A13 transcript variant X12 XM_047427410.1:c.274= XM_047427410.1:c.274G>T
S100A13 transcript variant X7 XM_047427406.1:c.274= XM_047427406.1:c.274G>T
S100A13 transcript variant X17 XM_047427433.1:c.274= XM_047427433.1:c.274G>T
S100A13 transcript variant X5 XM_047427404.1:c.274= XM_047427404.1:c.274G>T
S100A13 transcript variant X18 XM_047427435.1:c.274= XM_047427435.1:c.274G>T
S100A13 transcript variant X13 XM_047427413.1:c.274= XM_047427413.1:c.274G>T
S100A13 transcript variant X22 XM_047427446.1:c.274= XM_047427446.1:c.274G>T
S100A13 transcript variant X14 XM_047427417.1:c.274= XM_047427417.1:c.274G>T
S100A13 transcript variant X15 XM_047427419.1:c.274= XM_047427419.1:c.274G>T
protein S100-A13 isoform X2 XP_011508164.1:p.Asp92= XP_011508164.1:p.Asp92Tyr
protein S100-A13 isoform X2 XP_005245491.1:p.Asp92= XP_005245491.1:p.Asp92Tyr
protein S100-A13 isoform X2 XP_016857524.1:p.Asp92= XP_016857524.1:p.Asp92Tyr
protein S100-A13 isoform X2 XP_016857523.1:p.Asp92= XP_016857523.1:p.Asp92Tyr
protein S100-A13 NP_005970.1:p.Asp92= NP_005970.1:p.Asp92Tyr
protein S100-A13 NP_001019381.1:p.Asp92= NP_001019381.1:p.Asp92Tyr
protein S100-A13 NP_001019384.1:p.Asp92= NP_001019384.1:p.Asp92Tyr
protein S100-A13 isoform X2 XP_016857525.1:p.Asp92= XP_016857525.1:p.Asp92Tyr
protein S100-A13 NP_001019383.1:p.Asp92= NP_001019383.1:p.Asp92Tyr
protein S100-A13 NP_001019382.1:p.Asp92= NP_001019382.1:p.Asp92Tyr
protein S100-A13 isoform X2 XP_047283365.1:p.Asp92= XP_047283365.1:p.Asp92Tyr
protein S100-A13 isoform X2 XP_047283357.1:p.Asp92= XP_047283357.1:p.Asp92Tyr
protein S100-A13 isoform X2 XP_047283395.1:p.Asp92= XP_047283395.1:p.Asp92Tyr
protein S100-A13 isoform X2 XP_047283400.1:p.Asp92= XP_047283400.1:p.Asp92Tyr
protein S100-A13 isoform X2 XP_047283401.1:p.Asp92= XP_047283401.1:p.Asp92Tyr
protein S100-A13 isoform X2 XP_047283363.1:p.Asp92= XP_047283363.1:p.Asp92Tyr
protein S100-A13 isoform X2 XP_047283364.1:p.Asp92= XP_047283364.1:p.Asp92Tyr
protein S100-A13 isoform X2 XP_047283366.1:p.Asp92= XP_047283366.1:p.Asp92Tyr
protein S100-A13 isoform X2 XP_047283362.1:p.Asp92= XP_047283362.1:p.Asp92Tyr
protein S100-A13 isoform X2 XP_047283389.1:p.Asp92= XP_047283389.1:p.Asp92Tyr
protein S100-A13 isoform X2 XP_047283360.1:p.Asp92= XP_047283360.1:p.Asp92Tyr
protein S100-A13 isoform X2 XP_047283391.1:p.Asp92= XP_047283391.1:p.Asp92Tyr
protein S100-A13 isoform X2 XP_047283369.1:p.Asp92= XP_047283369.1:p.Asp92Tyr
protein S100-A13 isoform X2 XP_047283402.1:p.Asp92= XP_047283402.1:p.Asp92Tyr
protein S100-A13 isoform X2 XP_047283373.1:p.Asp92= XP_047283373.1:p.Asp92Tyr
protein S100-A13 isoform X2 XP_047283375.1:p.Asp92= XP_047283375.1:p.Asp92Tyr
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#.

2 SubSNP, 2 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss2746445505 Nov 08, 2017 (151)
2 GNOMAD ss2761239126 Nov 08, 2017 (151)
3 gnomAD - Genomes NC_000001.11 - 153618918 Apr 25, 2021 (155)
4 ALFA NC_000001.11 - 153618918 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
ss2746445505, ss2761239126 NC_000001.10:153591393:C:A NC_000001.11:153618917:C:A (self)
26851967, 2745185172 NC_000001.11:153618917:C:A NC_000001.11:153618917:C:A (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 rs1476802388

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