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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.

rs1257581794

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:153626437 (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>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000004 (1/264690, TOPMED)
A=0.000007 (1/140260, GnomAD)
A=0.00000 (0/14050, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
S100A13 : Synonymous Variant
S100A1 : 2KB Upstream 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 14050 G=1.00000 A=0.00000 1.0 0.0 0.0 N/A
European Sub 9690 G=1.0000 A=0.0000 1.0 0.0 0.0 N/A
African Sub 2898 G=1.0000 A=0.0000 1.0 0.0 0.0 N/A
African Others Sub 114 G=1.000 A=0.000 1.0 0.0 0.0 N/A
African American Sub 2784 G=1.0000 A=0.0000 1.0 0.0 0.0 N/A
Asian Sub 112 G=1.000 A=0.000 1.0 0.0 0.0 N/A
East Asian Sub 86 G=1.00 A=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 26 G=1.00 A=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 G=1.000 A=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 G=1.000 A=0.000 1.0 0.0 0.0 N/A
South Asian Sub 98 G=1.00 A=0.00 1.0 0.0 0.0 N/A
Other Sub 496 G=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
TopMed Global Study-wide 264690 G=0.999996 A=0.000004
gnomAD - Genomes Global Study-wide 140260 G=0.999993 A=0.000007
gnomAD - Genomes European Sub 75954 G=0.99999 A=0.00001
gnomAD - Genomes African Sub 42046 G=1.00000 A=0.00000
gnomAD - Genomes American Sub 13654 G=1.00000 A=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3322 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3134 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2150 G=1.0000 A=0.0000
Allele Frequency Aggregator Total Global 14050 G=1.00000 A=0.00000
Allele Frequency Aggregator European Sub 9690 G=1.0000 A=0.0000
Allele Frequency Aggregator African Sub 2898 G=1.0000 A=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 G=1.000 A=0.000
Allele Frequency Aggregator Other Sub 496 G=1.000 A=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 G=1.000 A=0.000
Allele Frequency Aggregator Asian Sub 112 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 98 G=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.153626437G>A
GRCh37.p13 chr 1 NC_000001.10:g.153598913G>A
Gene: S100A1, S100 calcium binding protein A1 (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
S100A1 transcript NM_006271.2:c. N/A Upstream Transcript Variant
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.36C>T S [TCC] > S [TCT] Coding Sequence Variant
protein S100-A13 NP_001019381.1:p.Ser12= S (Ser) > S (Ser) Synonymous Variant
S100A13 transcript variant 4 NM_001024212.2:c.36C>T S [TCC] > S [TCT] Coding Sequence Variant
protein S100-A13 NP_001019383.1:p.Ser12= S (Ser) > S (Ser) Synonymous Variant
S100A13 transcript variant 5 NM_001024213.2:c.36C>T S [TCC] > S [TCT] Coding Sequence Variant
protein S100-A13 NP_001019384.1:p.Ser12= S (Ser) > S (Ser) Synonymous Variant
S100A13 transcript variant 3 NM_001024211.2:c.36C>T S [TCC] > S [TCT] Coding Sequence Variant
protein S100-A13 NP_001019382.1:p.Ser12= S (Ser) > S (Ser) Synonymous Variant
S100A13 transcript variant 2 NM_005979.3:c.36C>T S [TCC] > S [TCT] Coding Sequence Variant
protein S100-A13 NP_005970.1:p.Ser12= S (Ser) > S (Ser) Synonymous Variant
S100A13 transcript variant X1 XM_047427400.1:c. N/A Genic Downstream Transcript Variant
S100A13 transcript variant X2 XM_047427401.1:c.36C>T S [TCC] > S [TCT] Coding Sequence Variant
protein S100-A13 isoform X2 XP_047283357.1:p.Ser12= S (Ser) > S (Ser) Synonymous Variant
S100A13 transcript variant X3 XM_011509862.4:c.36C>T S [TCC] > S [TCT] Coding Sequence Variant
protein S100-A13 isoform X2 XP_011508164.1:p.Ser12= S (Ser) > S (Ser) Synonymous Variant
S100A13 transcript variant X4 XM_005245434.4:c.36C>T S [TCC] > S [TCT] Coding Sequence Variant
protein S100-A13 isoform X2 XP_005245491.1:p.Ser12= S (Ser) > S (Ser) Synonymous Variant
S100A13 transcript variant X5 XM_047427404.1:c.36C>T S [TCC] > S [TCT] Coding Sequence Variant
protein S100-A13 isoform X2 XP_047283360.1:p.Ser12= S (Ser) > S (Ser) Synonymous Variant
S100A13 transcript variant X6 XM_017002034.3:c.36C>T S [TCC] > S [TCT] Coding Sequence Variant
protein S100-A13 isoform X2 XP_016857523.1:p.Ser12= S (Ser) > S (Ser) Synonymous Variant
S100A13 transcript variant X7 XM_047427406.1:c.36C>T S [TCC] > S [TCT] Coding Sequence Variant
protein S100-A13 isoform X2 XP_047283362.1:p.Ser12= S (Ser) > S (Ser) Synonymous Variant
S100A13 transcript variant X8 XM_047427407.1:c.36C>T S [TCC] > S [TCT] Coding Sequence Variant
protein S100-A13 isoform X2 XP_047283363.1:p.Ser12= S (Ser) > S (Ser) Synonymous Variant
S100A13 transcript variant X9 XM_047427408.1:c.36C>T S [TCC] > S [TCT] Coding Sequence Variant
protein S100-A13 isoform X2 XP_047283364.1:p.Ser12= S (Ser) > S (Ser) Synonymous Variant
S100A13 transcript variant X10 XM_047427409.1:c.36C>T S [TCC] > S [TCT] Coding Sequence Variant
protein S100-A13 isoform X2 XP_047283365.1:p.Ser12= S (Ser) > S (Ser) Synonymous Variant
S100A13 transcript variant X11 XM_017002035.3:c.36C>T S [TCC] > S [TCT] Coding Sequence Variant
protein S100-A13 isoform X2 XP_016857524.1:p.Ser12= S (Ser) > S (Ser) Synonymous Variant
S100A13 transcript variant X12 XM_047427410.1:c.36C>T S [TCC] > S [TCT] Coding Sequence Variant
protein S100-A13 isoform X2 XP_047283366.1:p.Ser12= S (Ser) > S (Ser) Synonymous Variant
S100A13 transcript variant X13 XM_047427413.1:c.36C>T S [TCC] > S [TCT] Coding Sequence Variant
protein S100-A13 isoform X2 XP_047283369.1:p.Ser12= S (Ser) > S (Ser) Synonymous Variant
S100A13 transcript variant X14 XM_047427417.1:c.36C>T S [TCC] > S [TCT] Coding Sequence Variant
protein S100-A13 isoform X2 XP_047283373.1:p.Ser12= S (Ser) > S (Ser) Synonymous Variant
S100A13 transcript variant X15 XM_047427419.1:c.36C>T S [TCC] > S [TCT] Coding Sequence Variant
protein S100-A13 isoform X2 XP_047283375.1:p.Ser12= S (Ser) > S (Ser) Synonymous Variant
S100A13 transcript variant X16 XM_017002036.2:c.36C>T S [TCC] > S [TCT] Coding Sequence Variant
protein S100-A13 isoform X2 XP_016857525.1:p.Ser12= S (Ser) > S (Ser) Synonymous Variant
S100A13 transcript variant X17 XM_047427433.1:c.36C>T S [TCC] > S [TCT] Coding Sequence Variant
protein S100-A13 isoform X2 XP_047283389.1:p.Ser12= S (Ser) > S (Ser) Synonymous Variant
S100A13 transcript variant X18 XM_047427435.1:c.36C>T S [TCC] > S [TCT] Coding Sequence Variant
protein S100-A13 isoform X2 XP_047283391.1:p.Ser12= S (Ser) > S (Ser) Synonymous Variant
S100A13 transcript variant X19 XM_047427439.1:c.36C>T S [TCC] > S [TCT] Coding Sequence Variant
protein S100-A13 isoform X2 XP_047283395.1:p.Ser12= S (Ser) > S (Ser) Synonymous Variant
S100A13 transcript variant X20 XM_047427444.1:c.36C>T S [TCC] > S [TCT] Coding Sequence Variant
protein S100-A13 isoform X2 XP_047283400.1:p.Ser12= S (Ser) > S (Ser) Synonymous Variant
S100A13 transcript variant X21 XM_047427445.1:c.36C>T S [TCC] > S [TCT] Coding Sequence Variant
protein S100-A13 isoform X2 XP_047283401.1:p.Ser12= S (Ser) > S (Ser) Synonymous Variant
S100A13 transcript variant X22 XM_047427446.1:c.36C>T S [TCC] > S [TCT] Coding Sequence Variant
protein S100-A13 isoform X2 XP_047283402.1:p.Ser12= S (Ser) > S (Ser) Synonymous 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= A
GRCh38.p14 chr 1 NC_000001.11:g.153626437= NC_000001.11:g.153626437G>A
GRCh37.p13 chr 1 NC_000001.10:g.153598913= NC_000001.10:g.153598913G>A
S100A13 transcript variant X3 XM_011509862.4:c.36= XM_011509862.4:c.36C>T
S100A13 transcript variant X1 XM_011509862.3:c.36= XM_011509862.3:c.36C>T
S100A13 transcript variant X1 XM_011509862.2:c.36= XM_011509862.2:c.36C>T
S100A13 transcript variant X1 XM_011509862.1:c.36= XM_011509862.1:c.36C>T
S100A13 transcript variant X4 XM_005245434.4:c.36= XM_005245434.4:c.36C>T
S100A13 transcript variant X4 XM_005245434.3:c.36= XM_005245434.3:c.36C>T
S100A13 transcript variant X2 XM_005245434.2:c.36= XM_005245434.2:c.36C>T
S100A13 transcript variant X2 XM_005245434.1:c.36= XM_005245434.1:c.36C>T
S100A13 transcript variant X11 XM_017002035.3:c.36= XM_017002035.3:c.36C>T
S100A13 transcript variant X6 XM_017002035.2:c.36= XM_017002035.2:c.36C>T
S100A13 transcript variant X6 XM_017002035.1:c.36= XM_017002035.1:c.36C>T
S100A13 transcript variant X6 XM_017002034.3:c.36= XM_017002034.3:c.36C>T
S100A13 transcript variant X3 XM_017002034.2:c.36= XM_017002034.2:c.36C>T
S100A13 transcript variant X3 XM_017002034.1:c.36= XM_017002034.1:c.36C>T
S100A13 transcript variant 2 NM_005979.3:c.36= NM_005979.3:c.36C>T
S100A13 transcript variant 2 NM_005979.2:c.36= NM_005979.2:c.36C>T
S100A13 transcript variant 1 NM_001024210.2:c.36= NM_001024210.2:c.36C>T
S100A13 transcript variant 1 NM_001024210.1:c.36= NM_001024210.1:c.36C>T
S100A13 transcript variant 5 NM_001024213.2:c.36= NM_001024213.2:c.36C>T
S100A13 transcript variant 5 NM_001024213.1:c.36= NM_001024213.1:c.36C>T
S100A13 transcript variant X16 XM_017002036.2:c.36= XM_017002036.2:c.36C>T
S100A13 transcript variant X7 XM_017002036.1:c.36= XM_017002036.1:c.36C>T
S100A13 transcript variant 4 NM_001024212.2:c.36= NM_001024212.2:c.36C>T
S100A13 transcript variant 4 NM_001024212.1:c.36= NM_001024212.1:c.36C>T
S100A13 transcript variant 3 NM_001024211.2:c.36= NM_001024211.2:c.36C>T
S100A13 transcript variant 3 NM_001024211.1:c.36= NM_001024211.1:c.36C>T
S100A13 transcript variant X10 XM_047427409.1:c.36= XM_047427409.1:c.36C>T
S100A13 transcript variant X2 XM_047427401.1:c.36= XM_047427401.1:c.36C>T
S100A13 transcript variant X19 XM_047427439.1:c.36= XM_047427439.1:c.36C>T
S100A13 transcript variant X20 XM_047427444.1:c.36= XM_047427444.1:c.36C>T
S100A13 transcript variant X21 XM_047427445.1:c.36= XM_047427445.1:c.36C>T
S100A13 transcript variant X8 XM_047427407.1:c.36= XM_047427407.1:c.36C>T
S100A13 transcript variant X9 XM_047427408.1:c.36= XM_047427408.1:c.36C>T
S100A13 transcript variant X12 XM_047427410.1:c.36= XM_047427410.1:c.36C>T
S100A13 transcript variant X7 XM_047427406.1:c.36= XM_047427406.1:c.36C>T
S100A13 transcript variant X17 XM_047427433.1:c.36= XM_047427433.1:c.36C>T
S100A13 transcript variant X5 XM_047427404.1:c.36= XM_047427404.1:c.36C>T
S100A13 transcript variant X18 XM_047427435.1:c.36= XM_047427435.1:c.36C>T
S100A13 transcript variant X13 XM_047427413.1:c.36= XM_047427413.1:c.36C>T
S100A13 transcript variant X22 XM_047427446.1:c.36= XM_047427446.1:c.36C>T
S100A13 transcript variant X14 XM_047427417.1:c.36= XM_047427417.1:c.36C>T
S100A13 transcript variant X15 XM_047427419.1:c.36= XM_047427419.1:c.36C>T
protein S100-A13 isoform X2 XP_011508164.1:p.Ser12= XP_011508164.1:p.Ser12=
protein S100-A13 isoform X2 XP_005245491.1:p.Ser12= XP_005245491.1:p.Ser12=
protein S100-A13 isoform X2 XP_016857524.1:p.Ser12= XP_016857524.1:p.Ser12=
protein S100-A13 isoform X2 XP_016857523.1:p.Ser12= XP_016857523.1:p.Ser12=
protein S100-A13 NP_005970.1:p.Ser12= NP_005970.1:p.Ser12=
protein S100-A13 NP_001019381.1:p.Ser12= NP_001019381.1:p.Ser12=
protein S100-A13 NP_001019384.1:p.Ser12= NP_001019384.1:p.Ser12=
protein S100-A13 isoform X2 XP_016857525.1:p.Ser12= XP_016857525.1:p.Ser12=
protein S100-A13 NP_001019383.1:p.Ser12= NP_001019383.1:p.Ser12=
protein S100-A13 NP_001019382.1:p.Ser12= NP_001019382.1:p.Ser12=
protein S100-A13 isoform X2 XP_047283365.1:p.Ser12= XP_047283365.1:p.Ser12=
protein S100-A13 isoform X2 XP_047283357.1:p.Ser12= XP_047283357.1:p.Ser12=
protein S100-A13 isoform X2 XP_047283395.1:p.Ser12= XP_047283395.1:p.Ser12=
protein S100-A13 isoform X2 XP_047283400.1:p.Ser12= XP_047283400.1:p.Ser12=
protein S100-A13 isoform X2 XP_047283401.1:p.Ser12= XP_047283401.1:p.Ser12=
protein S100-A13 isoform X2 XP_047283363.1:p.Ser12= XP_047283363.1:p.Ser12=
protein S100-A13 isoform X2 XP_047283364.1:p.Ser12= XP_047283364.1:p.Ser12=
protein S100-A13 isoform X2 XP_047283366.1:p.Ser12= XP_047283366.1:p.Ser12=
protein S100-A13 isoform X2 XP_047283362.1:p.Ser12= XP_047283362.1:p.Ser12=
protein S100-A13 isoform X2 XP_047283389.1:p.Ser12= XP_047283389.1:p.Ser12=
protein S100-A13 isoform X2 XP_047283360.1:p.Ser12= XP_047283360.1:p.Ser12=
protein S100-A13 isoform X2 XP_047283391.1:p.Ser12= XP_047283391.1:p.Ser12=
protein S100-A13 isoform X2 XP_047283369.1:p.Ser12= XP_047283369.1:p.Ser12=
protein S100-A13 isoform X2 XP_047283402.1:p.Ser12= XP_047283402.1:p.Ser12=
protein S100-A13 isoform X2 XP_047283373.1:p.Ser12= XP_047283373.1:p.Ser12=
protein S100-A13 isoform X2 XP_047283375.1:p.Ser12= XP_047283375.1:p.Ser12=
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, 3 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss4003613947 Apr 25, 2021 (155)
2 TOPMED ss4468073010 Apr 25, 2021 (155)
3 gnomAD - Genomes NC_000001.11 - 153626437 Apr 25, 2021 (155)
4 TopMed NC_000001.11 - 153626437 Apr 25, 2021 (155)
5 ALFA NC_000001.11 - 153626437 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
26853461, 31679345, 6677978385, ss4003613947, ss4468073010 NC_000001.11:153626436:G:A NC_000001.11:153626436:G: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 rs1257581794

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