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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.

rs553492964

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr10:43112106 (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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000038 (10/264690, TOPMED)
T=0.000018 (4/226778, GnomAD_exome)
T=0.000093 (13/140302, GnomAD) (+ 7 more)
T=0.00006 (3/50560, ExAC)
T=0.00007 (1/14050, ALFA)
T=0.0006 (4/6404, 1000G_30x)
T=0.0004 (2/5008, 1000G)
T=0.0011 (2/1832, Korea1K)
C=0.5 (1/2, SGDP_PRJ)
T=0.5 (1/2, SGDP_PRJ)
Clinical Significance
Reported in ClinVar
Gene : Consequence
RET : 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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 14050 C=0.99993 T=0.00007
European Sub 9690 C=1.0000 T=0.0000
African Sub 2898 C=1.0000 T=0.0000
African Others Sub 114 C=1.000 T=0.000
African American Sub 2784 C=1.0000 T=0.0000
Asian Sub 112 C=1.000 T=0.000
East Asian Sub 86 C=1.00 T=0.00
Other Asian Sub 26 C=1.00 T=0.00
Latin American 1 Sub 146 C=0.993 T=0.007
Latin American 2 Sub 610 C=1.000 T=0.000
South Asian Sub 98 C=1.00 T=0.00
Other Sub 496 C=1.000 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
TopMed Global Study-wide 264690 C=0.999962 T=0.000038
gnomAD - Exomes Global Study-wide 226778 C=0.999982 T=0.000018
gnomAD - Exomes European Sub 120088 C=1.000000 T=0.000000
gnomAD - Exomes Asian Sub 45050 C=1.00000 T=0.00000
gnomAD - Exomes American Sub 32604 C=1.00000 T=0.00000
gnomAD - Exomes African Sub 13872 C=0.99978 T=0.00022
gnomAD - Exomes Ashkenazi Jewish Sub 9538 C=1.0000 T=0.0000
gnomAD - Exomes Other Sub 5626 C=0.9998 T=0.0002
gnomAD - Genomes Global Study-wide 140302 C=0.999907 T=0.000093
gnomAD - Genomes European Sub 75962 C=1.00000 T=0.00000
gnomAD - Genomes African Sub 42062 C=0.99969 T=0.00031
gnomAD - Genomes American Sub 13670 C=1.00000 T=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3322 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3132 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2154 C=1.0000 T=0.0000
ExAC Global Study-wide 50560 C=0.99994 T=0.00006
ExAC Europe Sub 28180 C=1.00000 T=0.00000
ExAC Asian Sub 13304 C=1.00000 T=0.00000
ExAC African Sub 4842 C=0.9996 T=0.0004
ExAC American Sub 3864 C=1.0000 T=0.0000
ExAC Other Sub 370 C=0.997 T=0.003
Allele Frequency Aggregator Total Global 14050 C=0.99993 T=0.00007
Allele Frequency Aggregator European Sub 9690 C=1.0000 T=0.0000
Allele Frequency Aggregator African Sub 2898 C=1.0000 T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 C=1.000 T=0.000
Allele Frequency Aggregator Other Sub 496 C=1.000 T=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 C=0.993 T=0.007
Allele Frequency Aggregator Asian Sub 112 C=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 98 C=1.00 T=0.00
1000Genomes_30x Global Study-wide 6404 C=0.9994 T=0.0006
1000Genomes_30x African Sub 1786 C=0.9978 T=0.0022
1000Genomes_30x Europe Sub 1266 C=1.0000 T=0.0000
1000Genomes_30x South Asian Sub 1202 C=1.0000 T=0.0000
1000Genomes_30x East Asian Sub 1170 C=1.0000 T=0.0000
1000Genomes_30x American Sub 980 C=1.000 T=0.000
1000Genomes Global Study-wide 5008 C=0.9996 T=0.0004
1000Genomes African Sub 1322 C=0.9985 T=0.0015
1000Genomes East Asian Sub 1008 C=1.0000 T=0.0000
1000Genomes Europe Sub 1006 C=1.0000 T=0.0000
1000Genomes South Asian Sub 978 C=1.000 T=0.000
1000Genomes American Sub 694 C=1.000 T=0.000
Korean Genome Project KOREAN Study-wide 1832 C=0.9989 T=0.0011
SGDP_PRJ Global Study-wide 2 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 10 NC_000010.11:g.43112106C>T
GRCh37.p13 chr 10 NC_000010.10:g.43607554C>T
RET RefSeqGene (LRG_518) NG_007489.1:g.40038C>T
Gene: RET, ret proto-oncogene (plus strand)
Molecule type Change Amino acid[Codon] SO Term
RET transcript variant 5 NM_001355216.1:c.768C>T A [GCC] > A [GCT] Coding Sequence Variant
proto-oncogene tyrosine-protein kinase receptor Ret isoform d NP_001342145.1:p.Ala256= A (Ala) > A (Ala) Synonymous Variant
RET transcript variant 2 NM_020975.6:c.1530C>T A [GCC] > A [GCT] Coding Sequence Variant
proto-oncogene tyrosine-protein kinase receptor Ret isoform a precursor NP_066124.1:p.Ala510= A (Ala) > A (Ala) Synonymous Variant
RET transcript variant 4 NM_020630.6:c.1530C>T A [GCC] > A [GCT] Coding Sequence Variant
proto-oncogene tyrosine-protein kinase receptor Ret isoform c precursor NP_065681.1:p.Ala510= A (Ala) > A (Ala) 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.

Allele: T (allele ID: 221961 )
ClinVar Accession Disease Names Clinical Significance
RCV000205208.9 Multiple endocrine neoplasia, type 2 Likely-Benign
RCV000409713.2 Multiple endocrine neoplasia, type 2b Likely-Benign
RCV000410799.2 Multiple endocrine neoplasia, type 2a Likely-Benign
RCV000576018.2 Hereditary cancer-predisposing syndrome Likely-Benign
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= T
GRCh38.p14 chr 10 NC_000010.11:g.43112106= NC_000010.11:g.43112106C>T
GRCh37.p13 chr 10 NC_000010.10:g.43607554= NC_000010.10:g.43607554C>T
RET RefSeqGene (LRG_518) NG_007489.1:g.40038= NG_007489.1:g.40038C>T
RET transcript variant 4 NM_020630.7:c.1530= NM_020630.7:c.1530C>T
RET transcript variant 4 NM_020630.6:c.1530= NM_020630.6:c.1530C>T
RET transcript variant 4 NM_020630.5:c.1530= NM_020630.5:c.1530C>T
RET transcript variant 4 NM_020630.4:c.1530= NM_020630.4:c.1530C>T
RET transcript variant 2 NM_020975.6:c.1530= NM_020975.6:c.1530C>T
RET transcript variant 2 NM_020975.5:c.1530= NM_020975.5:c.1530C>T
RET transcript variant 2 NM_020975.4:c.1530= NM_020975.4:c.1530C>T
RET transcript variant 5 NM_001355216.2:c.768= NM_001355216.2:c.768C>T
RET transcript variant 5 NM_001355216.1:c.768= NM_001355216.1:c.768C>T
RET transcript variant 11 NM_001406764.1:c.1401= NM_001406764.1:c.1401C>T
RET transcript variant 12 NM_001406765.1:c.1530= NM_001406765.1:c.1530C>T
RET transcript variant 15 NM_001406768.1:c.1401= NM_001406768.1:c.1401C>T
RET transcript variant 17 NM_001406770.1:c.1242= NM_001406770.1:c.1242C>T
RET transcript variant 19 NM_001406772.1:c.1134= NM_001406772.1:c.1134C>T
RET transcript variant 20 NM_001406773.1:c.1092= NM_001406773.1:c.1092C>T
RET transcript variant 21 NM_001406774.1:c.1005= NM_001406774.1:c.1005C>T
RET transcript variant 25 NM_001406778.1:c.804= NM_001406778.1:c.804C>T
RET transcript variant 29 NM_001406782.1:c.633= NM_001406782.1:c.633C>T
RET transcript variant 31 NM_001406784.1:c.540= NM_001406784.1:c.540C>T
RET transcript variant 32 NM_001406785.1:c.633= NM_001406785.1:c.633C>T
RET transcript variant 33 NM_001406786.1:c.504= NM_001406786.1:c.504C>T
RET transcript variant 34 NM_001406787.1:c.633= NM_001406787.1:c.633C>T
RET transcript variant 37 NM_001406790.1:c.345= NM_001406790.1:c.345C>T
RET transcript variant 38 NM_001406791.1:c.345= NM_001406791.1:c.345C>T
RET transcript variant 41 NM_001406794.1:c.81= NM_001406794.1:c.81C>T
RET transcript variant 6 NM_001406759.1:c.1530= NM_001406759.1:c.1530C>T
RET transcript variant 9 NM_001406762.1:c.1401= NM_001406762.1:c.1401C>T
RET transcript variant 10 NM_001406763.1:c.1530= NM_001406763.1:c.1530C>T
RET transcript variant 13 NM_001406766.1:c.1242= NM_001406766.1:c.1242C>T
RET transcript variant 18 NM_001406771.1:c.1092= NM_001406771.1:c.1092C>T
RET transcript variant 22 NM_001406775.1:c.804= NM_001406775.1:c.804C>T
RET transcript variant 24 NM_001406777.1:c.804= NM_001406777.1:c.804C>T
RET transcript variant 27 NM_001406780.1:c.633= NM_001406780.1:c.633C>T
RET transcript variant 30 NM_001406783.1:c.504= NM_001406783.1:c.504C>T
RET transcript variant 35 NM_001406788.1:c.345= NM_001406788.1:c.345C>T
RET transcript variant 1 NM_001406743.1:c.1530= NM_001406743.1:c.1530C>T
RET transcript variant 7 NM_001406760.1:c.1530= NM_001406760.1:c.1530C>T
RET transcript variant 8 NM_001406761.1:c.1401= NM_001406761.1:c.1401C>T
RET transcript variant 3 NM_001406744.1:c.1530= NM_001406744.1:c.1530C>T
RET transcript variant 39 NM_001406792.1:c.81= NM_001406792.1:c.81C>T
RET transcript variant 14 NM_001406767.1:c.1242= NM_001406767.1:c.1242C>T
RET transcript variant 16 NM_001406769.1:c.1134= NM_001406769.1:c.1134C>T
RET transcript variant 26 NM_001406779.1:c.633= NM_001406779.1:c.633C>T
RET transcript variant 23 NM_001406776.1:c.804= NM_001406776.1:c.804C>T
RET transcript variant 28 NM_001406781.1:c.633= NM_001406781.1:c.633C>T
RET transcript variant 36 NM_001406789.1:c.345= NM_001406789.1:c.345C>T
RET transcript variant 40 NM_001406793.1:c.81= NM_001406793.1:c.81C>T
RET transcript variant 1 NM_000323.2:c.1530= NM_000323.2:c.1530C>T
RET transcript variant 3 NM_020629.2:c.1530= NM_020629.2:c.1530C>T
RET transcript variant 1 NM_000323.1:c.1530= NM_000323.1:c.1530C>T
RET transcript variant 3 NM_020629.1:c.1530= NM_020629.1:c.1530C>T
proto-oncogene tyrosine-protein kinase receptor Ret isoform c precursor NP_065681.1:p.Ala510= NP_065681.1:p.Ala510=
proto-oncogene tyrosine-protein kinase receptor Ret isoform a precursor NP_066124.1:p.Ala510= NP_066124.1:p.Ala510=
proto-oncogene tyrosine-protein kinase receptor Ret isoform d NP_001342145.1:p.Ala256= NP_001342145.1:p.Ala256=
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, 9 Frequency, 4 ClinVar submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss1337187928 Aug 21, 2014 (142)
2 EVA_EXAC ss1689879460 Apr 01, 2015 (144)
3 HUMAN_LONGEVITY ss2174314512 Dec 20, 2016 (150)
4 GNOMAD ss2738209716 Nov 08, 2017 (151)
5 GNOMAD ss2748376387 Nov 08, 2017 (151)
6 GNOMAD ss2888038179 Nov 08, 2017 (151)
7 SGDP_PRJ ss3874040263 Apr 26, 2020 (154)
8 KOGIC ss3967752849 Apr 26, 2020 (154)
9 TOPMED ss4850230247 Apr 26, 2021 (155)
10 1000G_HIGH_COVERAGE ss5283797330 Oct 16, 2022 (156)
11 EVA ss5393040404 Oct 16, 2022 (156)
12 1000G_HIGH_COVERAGE ss5577610318 Oct 16, 2022 (156)
13 EVA ss5878662359 Oct 16, 2022 (156)
14 1000Genomes NC_000010.10 - 43607554 Oct 12, 2018 (152)
15 1000Genomes_30x NC_000010.11 - 43112106 Oct 16, 2022 (156)
16 ExAC NC_000010.10 - 43607554 Oct 12, 2018 (152)
17 gnomAD - Genomes NC_000010.11 - 43112106 Apr 26, 2021 (155)
18 gnomAD - Exomes NC_000010.10 - 43607554 Jul 13, 2019 (153)
19 Korean Genome Project NC_000010.11 - 43112106 Apr 26, 2020 (154)
20 SGDP_PRJ NC_000010.10 - 43607554 Apr 26, 2020 (154)
21 TopMed NC_000010.11 - 43112106 Apr 26, 2021 (155)
22 ALFA NC_000010.11 - 43112106 Apr 26, 2021 (155)
23 ClinVar RCV000205208.9 Oct 16, 2022 (156)
24 ClinVar RCV000409713.2 Oct 16, 2022 (156)
25 ClinVar RCV000410799.2 Oct 16, 2022 (156)
26 ClinVar RCV000576018.2 Oct 16, 2022 (156)
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
49566518, 98907, 7407563, 26057243, ss1337187928, ss1689879460, ss2738209716, ss2748376387, ss2888038179, ss3874040263, ss5393040404 NC_000010.10:43607553:C:T NC_000010.11:43112105:C:T (self)
RCV000205208.9, RCV000409713.2, RCV000410799.2, RCV000576018.2, 65136253, 350304637, 24130850, 65775902, 14903581439, ss2174314512, ss3967752849, ss4850230247, ss5283797330, ss5577610318, ss5878662359 NC_000010.11:43112105:C:T NC_000010.11:43112105: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 rs553492964

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