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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.

rs1484929183

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr16:547636 (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
A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000004 (1/264690, TOPMED)
T=0.000007 (1/140182, GnomAD)
T=0.00000 (0/14050, ALFA) (+ 3 more)
T=0.0003 (2/6404, 1000G_30x)
A=0.5 (1/2, SGDP_PRJ)
T=0.5 (1/2, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CAPN15 : Synonymous 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 A=1.00000 T=0.00000 1.0 0.0 0.0 N/A
European Sub 9690 A=1.0000 T=0.0000 1.0 0.0 0.0 N/A
African Sub 2898 A=1.0000 T=0.0000 1.0 0.0 0.0 N/A
African Others Sub 114 A=1.000 T=0.000 1.0 0.0 0.0 N/A
African American Sub 2784 A=1.0000 T=0.0000 1.0 0.0 0.0 N/A
Asian Sub 112 A=1.000 T=0.000 1.0 0.0 0.0 N/A
East Asian Sub 86 A=1.00 T=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 26 A=1.00 T=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 A=1.000 T=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 A=1.000 T=0.000 1.0 0.0 0.0 N/A
South Asian Sub 98 A=1.00 T=0.00 1.0 0.0 0.0 N/A
Other Sub 496 A=1.000 T=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 A=0.999996 T=0.000004
gnomAD - Genomes Global Study-wide 140182 A=0.999993 T=0.000007
gnomAD - Genomes European Sub 75922 A=1.00000 T=0.00000
gnomAD - Genomes African Sub 41988 A=0.99998 T=0.00002
gnomAD - Genomes American Sub 13666 A=1.00000 T=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3324 A=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3130 A=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2152 A=1.0000 T=0.0000
Allele Frequency Aggregator Total Global 14050 A=1.00000 T=0.00000
Allele Frequency Aggregator European Sub 9690 A=1.0000 T=0.0000
Allele Frequency Aggregator African Sub 2898 A=1.0000 T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 A=1.000 T=0.000
Allele Frequency Aggregator Other Sub 496 A=1.000 T=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 A=1.000 T=0.000
Allele Frequency Aggregator Asian Sub 112 A=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 98 A=1.00 T=0.00
1000Genomes_30x Global Study-wide 6404 A=0.9997 T=0.0003
1000Genomes_30x African Sub 1786 A=0.9989 T=0.0011
1000Genomes_30x Europe Sub 1266 A=1.0000 T=0.0000
1000Genomes_30x South Asian Sub 1202 A=1.0000 T=0.0000
1000Genomes_30x East Asian Sub 1170 A=1.0000 T=0.0000
1000Genomes_30x American Sub 980 A=1.000 T=0.000
SGDP_PRJ Global Study-wide 2 A=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 16 NC_000016.10:g.547636A>T
GRCh37.p13 chr 16 NC_000016.9:g.597636A>T
Gene: CAPN15, calpain 15 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
CAPN15 transcript NM_005632.3:c.798A>T S [TCA] > S [TCT] Coding Sequence Variant
calpain-15 NP_005623.1:p.Ser266= S (Ser) > S (Ser) Synonymous Variant
CAPN15 transcript variant X1 XM_047434525.1:c.1002A>T S [TCA] > S [TCT] Coding Sequence Variant
calpain-15 isoform X1 XP_047290481.1:p.Ser334= S (Ser) > S (Ser) Synonymous Variant
CAPN15 transcript variant X2 XM_047434526.1:c.1002A>T S [TCA] > S [TCT] Coding Sequence Variant
calpain-15 isoform X1 XP_047290482.1:p.Ser334= S (Ser) > S (Ser) Synonymous Variant
CAPN15 transcript variant X3 XM_047434527.1:c.1002A>T S [TCA] > S [TCT] Coding Sequence Variant
calpain-15 isoform X1 XP_047290483.1:p.Ser334= S (Ser) > S (Ser) Synonymous Variant
CAPN15 transcript variant X4 XM_047434528.1:c.1002A>T S [TCA] > S [TCT] Coding Sequence Variant
calpain-15 isoform X1 XP_047290484.1:p.Ser334= S (Ser) > S (Ser) Synonymous Variant
CAPN15 transcript variant X5 XM_011522625.3:c.1002A>T S [TCA] > S [TCT] Coding Sequence Variant
calpain-15 isoform X1 XP_011520927.1:p.Ser334= S (Ser) > S (Ser) Synonymous Variant
CAPN15 transcript variant X6 XM_047434529.1:c.1002A>T S [TCA] > S [TCT] Coding Sequence Variant
calpain-15 isoform X2 XP_047290485.1:p.Ser334= S (Ser) > S (Ser) Synonymous Variant
CAPN15 transcript variant X7 XM_047434530.1:c.1002A>T S [TCA] > S [TCT] Coding Sequence Variant
calpain-15 isoform X3 XP_047290486.1:p.Ser334= S (Ser) > S (Ser) Synonymous Variant
CAPN15 transcript variant X8 XM_047434531.1:c.798A>T S [TCA] > S [TCT] Coding Sequence Variant
calpain-15 isoform X4 XP_047290487.1:p.Ser266= S (Ser) > S (Ser) Synonymous Variant
CAPN15 transcript variant X9 XM_011522631.3:c.798A>T S [TCA] > S [TCT] Coding Sequence Variant
calpain-15 isoform X4 XP_011520933.1:p.Ser266= S (Ser) > S (Ser) Synonymous Variant
CAPN15 transcript variant X10 XM_011522628.4:c.798A>T S [TCA] > S [TCT] Coding Sequence Variant
calpain-15 isoform X4 XP_011520930.1:p.Ser266= S (Ser) > S (Ser) Synonymous Variant
CAPN15 transcript variant X11 XM_011522629.4:c.798A>T S [TCA] > S [TCT] Coding Sequence Variant
calpain-15 isoform X4 XP_011520931.1:p.Ser266= S (Ser) > S (Ser) Synonymous Variant
CAPN15 transcript variant X12 XM_047434532.1:c.798A>T S [TCA] > S [TCT] Coding Sequence Variant
calpain-15 isoform X4 XP_047290488.1:p.Ser266= S (Ser) > S (Ser) Synonymous Variant
CAPN15 transcript variant X13 XM_047434533.1:c.798A>T S [TCA] > S [TCT] Coding Sequence Variant
calpain-15 isoform X5 XP_047290489.1:p.Ser266= S (Ser) > S (Ser) Synonymous Variant
CAPN15 transcript variant X14 XM_047434534.1:c.999A>T S [TCA] > S [TCT] Coding Sequence Variant
calpain-15 isoform X6 XP_047290490.1:p.Ser333= S (Ser) > S (Ser) Synonymous Variant
CAPN15 transcript variant X15 XM_047434535.1:c.798A>T S [TCA] > S [TCT] Coding Sequence Variant
calpain-15 isoform X7 XP_047290491.1:p.Ser266= 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 A= T
GRCh38.p14 chr 16 NC_000016.10:g.547636= NC_000016.10:g.547636A>T
GRCh37.p13 chr 16 NC_000016.9:g.597636= NC_000016.9:g.597636A>T
CAPN15 transcript variant X10 XM_011522628.4:c.798= XM_011522628.4:c.798A>T
CAPN15 transcript variant X10 XM_011522628.3:c.798= XM_011522628.3:c.798A>T
CAPN15 transcript variant X10 XM_011522628.2:c.798= XM_011522628.2:c.798A>T
CAPN15 transcript variant X10 XM_011522628.1:c.798= XM_011522628.1:c.798A>T
CAPN15 transcript variant X11 XM_011522629.4:c.798= XM_011522629.4:c.798A>T
CAPN15 transcript variant X11 XM_011522629.3:c.798= XM_011522629.3:c.798A>T
CAPN15 transcript variant X11 XM_011522629.2:c.798= XM_011522629.2:c.798A>T
CAPN15 transcript variant X11 XM_011522629.1:c.798= XM_011522629.1:c.798A>T
CAPN15 transcript variant X5 XM_011522625.3:c.1002= XM_011522625.3:c.1002A>T
CAPN15 transcript variant X7 XM_011522625.2:c.1002= XM_011522625.2:c.1002A>T
CAPN15 transcript variant X7 XM_011522625.1:c.1002= XM_011522625.1:c.1002A>T
CAPN15 transcript NM_005632.3:c.798= NM_005632.3:c.798A>T
CAPN15 transcript NM_005632.2:c.798= NM_005632.2:c.798A>T
CAPN15 transcript variant X9 XM_011522631.3:c.798= XM_011522631.3:c.798A>T
CAPN15 transcript variant X13 XM_011522631.2:c.798= XM_011522631.2:c.798A>T
CAPN15 transcript variant X13 XM_011522631.1:c.798= XM_011522631.1:c.798A>T
CAPN15 transcript variant X14 XM_047434534.1:c.999= XM_047434534.1:c.999A>T
CAPN15 transcript variant X1 XM_047434525.1:c.1002= XM_047434525.1:c.1002A>T
CAPN15 transcript variant X7 XM_047434530.1:c.1002= XM_047434530.1:c.1002A>T
CAPN15 transcript variant X2 XM_047434526.1:c.1002= XM_047434526.1:c.1002A>T
CAPN15 transcript variant X3 XM_047434527.1:c.1002= XM_047434527.1:c.1002A>T
CAPN15 transcript variant X4 XM_047434528.1:c.1002= XM_047434528.1:c.1002A>T
CAPN15 transcript variant X6 XM_047434529.1:c.1002= XM_047434529.1:c.1002A>T
CAPN15 transcript variant X13 XM_047434533.1:c.798= XM_047434533.1:c.798A>T
CAPN15 transcript variant X15 XM_047434535.1:c.798= XM_047434535.1:c.798A>T
CAPN15 transcript variant X8 XM_047434531.1:c.798= XM_047434531.1:c.798A>T
CAPN15 transcript variant X12 XM_047434532.1:c.798= XM_047434532.1:c.798A>T
calpain-15 isoform X4 XP_011520930.1:p.Ser266= XP_011520930.1:p.Ser266=
calpain-15 isoform X4 XP_011520931.1:p.Ser266= XP_011520931.1:p.Ser266=
calpain-15 isoform X1 XP_011520927.1:p.Ser334= XP_011520927.1:p.Ser334=
calpain-15 NP_005623.1:p.Ser266= NP_005623.1:p.Ser266=
calpain-15 isoform X4 XP_011520933.1:p.Ser266= XP_011520933.1:p.Ser266=
calpain-15 isoform X6 XP_047290490.1:p.Ser333= XP_047290490.1:p.Ser333=
calpain-15 isoform X1 XP_047290481.1:p.Ser334= XP_047290481.1:p.Ser334=
calpain-15 isoform X3 XP_047290486.1:p.Ser334= XP_047290486.1:p.Ser334=
calpain-15 isoform X1 XP_047290482.1:p.Ser334= XP_047290482.1:p.Ser334=
calpain-15 isoform X1 XP_047290483.1:p.Ser334= XP_047290483.1:p.Ser334=
calpain-15 isoform X1 XP_047290484.1:p.Ser334= XP_047290484.1:p.Ser334=
calpain-15 isoform X2 XP_047290485.1:p.Ser334= XP_047290485.1:p.Ser334=
calpain-15 isoform X5 XP_047290489.1:p.Ser266= XP_047290489.1:p.Ser266=
calpain-15 isoform X7 XP_047290491.1:p.Ser266= XP_047290491.1:p.Ser266=
calpain-15 isoform X4 XP_047290487.1:p.Ser266= XP_047290487.1:p.Ser266=
calpain-15 isoform X4 XP_047290488.1:p.Ser266= XP_047290488.1:p.Ser266=
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#.

6 SubSNP, 5 Frequency submissions
No Submitter Submission ID Date (Build)
1 SGDP_PRJ ss3883720104 Apr 27, 2020 (154)
2 GNOMAD ss4295263068 Apr 26, 2021 (155)
3 TOPMED ss5004389572 Apr 26, 2021 (155)
4 1000G_HIGH_COVERAGE ss5299772396 Oct 16, 2022 (156)
5 1000G_HIGH_COVERAGE ss5601830851 Oct 16, 2022 (156)
6 SANFORD_IMAGENETICS ss5658263028 Oct 16, 2022 (156)
7 1000Genomes_30x NC_000016.10 - 547636 Oct 16, 2022 (156)
8 gnomAD - Genomes NC_000016.10 - 547636 Apr 26, 2021 (155)
9 SGDP_PRJ NC_000016.9 - 597636 Apr 27, 2020 (154)
10 TopMed NC_000016.10 - 547636 Apr 26, 2021 (155)
11 ALFA NC_000016.10 - 547636 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
35737084, ss3883720104, ss5658263028 NC_000016.9:597635:A:T NC_000016.10:547635:A:T (self)
89356786, 479953310, 219935233, 7795942109, ss4295263068, ss5004389572, ss5299772396, ss5601830851 NC_000016.10:547635:A:T NC_000016.10:547635: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 rs1484929183

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