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dbSNP Short Genetic Variations

Reference SNP (rs) Report

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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.

rs77724903

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr10:43118460 (GRCh38.p7) 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>G / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.00209 (515/246068, GnomAD)
T=0.00121 (152/125568, TOPMED)
T=0.00180 (216/119802, ExAC) (+ 4 more)
T=0.0026 (80/30956, GnomAD)
T=0.000 (1/5008, 1000G)
T=0.001 (2/3854, ALSPAC)
T=0.000 (0/3708, TWINSUK)
Clinical Significance
Reported in ClinVar
Gene : Consequence
RET : Missense Variant
Publications
14 citations
Genomic View
See rs on genome
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.p7 chr 10 NC_000010.11:g.43118460A>G
GRCh38.p7 chr 10 NC_000010.11:g.43118460A>T
GRCh37.p13 chr 10 NC_000010.10:g.43613908A>G
GRCh37.p13 chr 10 NC_000010.10:g.43613908A>T
RET RefSeqGene (LRG_518) NG_007489.1:g.46392A>G
RET RefSeqGene (LRG_518) NG_007489.1:g.46392A>T
Gene: RET, ret proto-oncogene (plus strand)
Molecule type Change Amino acid[Codon] SO Term
RET transcript variant 2 NM_020975.4:c.237...

NM_020975.4:c.2372A>G

Y [TAT] > C [TGT] Coding Sequence Variant
proto-oncogene tyrosine-protein kinase receptor Ret isoform a precursor NP_066124.1:p.Tyr...

NP_066124.1:p.Tyr791Cys

Y (Tyr) > C (Cys) Missense Variant
RET transcript variant 2 NM_020975.4:c.237...

NM_020975.4:c.2372A>T

Y [TAT] > F [TTT] Coding Sequence Variant
proto-oncogene tyrosine-protein kinase receptor Ret isoform a precursor NP_066124.1:p.Tyr...

NP_066124.1:p.Tyr791Phe

Y (Tyr) > F (Phe) Missense Variant
RET transcript variant 4 NM_020630.4:c.237...

NM_020630.4:c.2372A>G

Y [TAT] > C [TGT] Coding Sequence Variant
proto-oncogene tyrosine-protein kinase receptor Ret isoform c precursor NP_065681.1:p.Tyr...

NP_065681.1:p.Tyr791Cys

Y (Tyr) > C (Cys) Missense Variant
RET transcript variant 4 NM_020630.4:c.237...

NM_020630.4:c.2372A>T

Y [TAT] > F [TTT] Coding Sequence Variant
proto-oncogene tyrosine-protein kinase receptor Ret isoform c precursor NP_065681.1:p.Tyr...

NP_065681.1:p.Tyr791Phe

Y (Tyr) > F (Phe) 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.

Allele: T (allele ID: 28975 )
ClinVar Accession Disease Names Clinical Significance
RCV000014962.26 Familial medullary thyroid carcinoma Pathogenic
RCV000014963.29 Pheochromocytoma Likely-Benign
RCV000021851.2 MEN2A and FMTC Pathogenic
RCV000034771.5 not provided Benign
RCV000123309.8 Multiple endocrine neoplasia, type 2 Benign
RCV000130367.4 Hereditary cancer-predisposing syndrome Likely-Benign
RCV000148769.1 Hirschsprung disease Likely-Benign
RCV000312825.1 Hirschsprung Disease, Dominant Likely-Benign
RCV000370653.1 Multiple endocrine neoplasia Likely-Benign
RCV000400976.1 Renal adysplasia Likely-Benign
RCV000419149.1 Medullary thyroid carcinoma Likely-Pathogenic
RCV000426589.1 Multiple endocrine neoplasia, type 4 Likely-Pathogenic
RCV000431156.1 Multiple endocrine neoplasia, type 2b Likely-Pathogenic
RCV000436831.1 Multiple endocrine neoplasia, type 2a Likely-Pathogenic
RCV000441584.1 Multiple endocrine neoplasia, type 1 Likely-Pathogenic
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
The Genome Aggregation Database Global Study-wide 246068 A=0.99790 T=0.00209, G=0.00000
The Genome Aggregation Database European Sub 133866 A=0.99748 T=0.00252, G=0.00000
The Genome Aggregation Database Asian Sub 48004 A=1.0000 T=0.0000, G=0.0000
The Genome Aggregation Database American Sub 33580 A=0.9999 T=0.0001, G=0.0000
The Genome Aggregation Database African Sub 15290 A=1.0000 T=0.0000, G=0.0000
The Genome Aggregation Database Ashkenazi Jewish Sub 9848 A=0.984 T=0.016, G=0.000
The Genome Aggregation Database Other Sub 5480 A=0.998 T=0.002, G=0.000
Trans-Omics for Precision Medicine Global Study-wide 125568 A=0.99879 T=0.00121
The Exome Aggregation Consortium Global Study-wide 119802 A=0.99820 T=0.00180
The Exome Aggregation Consortium Europe Sub 72374 A=0.9971 T=0.0029
The Exome Aggregation Consortium Asian Sub 24942 A=1.0000 T=0.0000
The Exome Aggregation Consortium American Sub 11422 A=0.9999 T=0.0001
The Exome Aggregation Consortium African Sub 10180 A=0.9999 T=0.0001
The Exome Aggregation Consortium Other Sub 884 A=1.00 T=0.00
The Genome Aggregation Database Global Study-wide 30956 A=0.9974 T=0.0026
The Genome Aggregation Database European Sub 18490 A=0.9963 T=0.0037
The Genome Aggregation Database African Sub 8728 A=1.000 T=0.000
The Genome Aggregation Database East Asian Sub 1620 A=1.000 T=0.000
The Genome Aggregation Database Other Sub 980 A=0.99 T=0.01
The Genome Aggregation Database American Sub 838 A=1.00 T=0.00
The Genome Aggregation Database Ashkenazi Jewish Sub 300 A=0.99 T=0.01
1000Genomes Global Study-wide 5008 A=1.000 T=0.000
1000Genomes African Sub 1322 A=1.000 T=0.000
1000Genomes East Asian Sub 1008 A=1.000 T=0.000
1000Genomes Europe Sub 1006 A=0.999 T=0.001
1000Genomes South Asian Sub 978 A=1.00 T=0.00
1000Genomes American Sub 694 A=1.00 T=0.00
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.999 T=0.001
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=1.000 T=0.000
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= G T Note
GRCh38.p7 chr 10 NC_000010.11:g.43...

NC_000010.11:g.43118460A=

NC_000010.11:g.43...

NC_000010.11:g.43118460A>G

NC_000010.11:g.43...

NC_000010.11:g.43118460A>T

GRCh37.p13 chr 10 NC_000010.10:g.43...

NC_000010.10:g.43613908A=

NC_000010.10:g.43...

NC_000010.10:g.43613908A>G

NC_000010.10:g.43...

NC_000010.10:g.43613908A>T

RET RefSeqGene (LRG_518) NG_007489.1:g.463...

NG_007489.1:g.46392A=

NG_007489.1:g.463...

NG_007489.1:g.46392A>G

NG_007489.1:g.463...

NG_007489.1:g.46392A>T

RET transcript variant 2 NM_020975.4:c.2372A= NM_020975.4:c.237...

NM_020975.4:c.2372A>G

NM_020975.4:c.237...

NM_020975.4:c.2372A>T

RET transcript variant 4 NM_020630.4:c.2372A= NM_020630.4:c.237...

NM_020630.4:c.2372A>G

NM_020630.4:c.237...

NM_020630.4:c.2372A>T

proto-oncogene tyrosine-protein kinase receptor Ret isoform a precursor NP_066124.1:p.Tyr...

NP_066124.1:p.Tyr791=

NP_066124.1:p.Tyr...

NP_066124.1:p.Tyr791Cys

NP_066124.1:p.Tyr...

NP_066124.1:p.Tyr791Phe

proto-oncogene tyrosine-protein kinase receptor Ret isoform c precursor NP_065681.1:p.Tyr...

NP_065681.1:p.Tyr791=

NP_065681.1:p.Tyr...

NP_065681.1:p.Tyr791Cys

NP_065681.1:p.Tyr...

NP_065681.1:p.Tyr791Phe

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#.

26 SubSNP, 15 ClinVar, 7 Frequency submissions
No Submitter Submission ID Date (Build)
1 OMIM-CURATED-RECORDS ss157383340 Dec 01, 2009 (131)
2 OMIM-CURATED-RECORDS ss275515845 Nov 29, 2010 (133)
3 NHLBI-ESP ss342296558 May 09, 2011 (134)
4 EXOME_CHIP ss491434467 May 04, 2012 (137)
5 CLINSEQ_SNP ss491624086 May 04, 2012 (137)
6 ILLUMINA ss780885789 Aug 21, 2014 (142)
7 ILLUMINA ss783571870 Aug 21, 2014 (142)
8 1000GENOMES ss1337188117 Aug 21, 2014 (142)
9 EVA_FINRISK ss1584067731 Apr 01, 2015 (144)
10 EVA_UK10K_ALSPAC ss1624447275 Apr 01, 2015 (144)
11 EVA_UK10K_TWINSUK ss1667441308 Apr 01, 2015 (144)
12 EVA_EXAC ss1689879703 Apr 01, 2015 (144)
13 EVA_MGP ss1711254896 Apr 01, 2015 (144)
14 ILLUMINA ss1751968430 Sep 08, 2015 (146)
15 ILLUMINA ss1917846292 Feb 12, 2016 (147)
16 ILLUMINA ss1946280886 Feb 12, 2016 (147)
17 ILLUMINA ss1959257000 Feb 12, 2016 (147)
18 HUMAN_LONGEVITY ss2174314930 Dec 20, 2016 (150)
19 TOPMED ss2337249696 Dec 20, 2016 (150)
20 GNOMAD ss2738210090 Nov 08, 2017 (151)
21 GNOMAD ss2748376498 Nov 08, 2017 (151)
22 GNOMAD ss2888038693 Nov 08, 2017 (151)
23 SWEGEN ss3006360783 Nov 08, 2017 (151)
24 ILLUMINA ss3021234231 Nov 08, 2017 (151)
25 TOPMED ss3118052380 Nov 08, 2017 (151)
26 ILLUMINA ss3626433939 Jul 20, 2018 (151)
27 1000Genomes NC_000010.10 - 43613908 Jul 20, 2018 (151)
28 The Avon Longitudinal Study of Parents and Children NC_000010.10 - 43613908 Jul 20, 2018 (151)
29 The Exome Aggregation Consortium NC_000010.10 - 43613908 Jul 20, 2018 (151)
30 The Genome Aggregation Database NC_000010.10 - 43613908 Jul 20, 2018 (151)
31 The Genome Aggregation Database NC_000010.10 - 43613908 Jul 20, 2018 (151)
32 Trans-Omics for Precision Medicine NC_000010.11 - 43118460 Jul 20, 2018 (151)
33 UK 10K study - Twins NC_000010.10 - 43613908 Jul 20, 2018 (151)
34 ClinVar RCV000014962.26 Jul 20, 2018 (151)
35 ClinVar RCV000014963.29 Jul 20, 2018 (151)
36 ClinVar RCV000021851.2 Jul 20, 2018 (151)
37 ClinVar RCV000034771.5 Jul 20, 2018 (151)
38 ClinVar RCV000123309.8 Jul 20, 2018 (151)
39 ClinVar RCV000130367.4 Jul 20, 2018 (151)
40 ClinVar RCV000148769.1 Jul 20, 2018 (151)
41 ClinVar RCV000312825.1 Jul 20, 2018 (151)
42 ClinVar RCV000370653.1 Jul 20, 2018 (151)
43 ClinVar RCV000400976.1 Jul 20, 2018 (151)
44 ClinVar RCV000419149.1 Jul 20, 2018 (151)
45 ClinVar RCV000426589.1 Jul 20, 2018 (151)
46 ClinVar RCV000431156.1 Jul 20, 2018 (151)
47 ClinVar RCV000436831.1 Jul 20, 2018 (151)
48 ClinVar RCV000441584.1 Jul 20, 2018 (151)
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
ss491624086 NC_000010.9:42933913:A= NC_000010.11:43118459:A= (self)
49566710, 27522679, 99160, 21740214, 7224825, 27522679, ss342296558, ss491434467, ss780885789, ss783571870, ss1337188117, ss1584067731, ss1624447275, ss1667441308, ss1689879703, ss1711254896, ss1751968430, ss1917846292, ss1946280886, ss1959257000, ss2337249696, ss2738210090, ss2748376498, ss2888038693, ss3006360783, ss3021234231, ss3626433939 NC_000010.10:43613907:A= NC_000010.11:43118459:A= (self)
41325788, ss157383340, ss275515845, ss2174314930, ss3118052380 NC_000010.11:43118459:A= NC_000010.11:43118459:A= (self)
7224825, ss2738210090 NC_000010.10:43613907:A>G NC_000010.11:43118459:A>G (self)
ss491624086 NC_000010.9:42933913:A>T NC_000010.11:43118459:A>T (self)
49566710, 27522679, 99160, 21740214, 7224825, 27522679, ss342296558, ss491434467, ss780885789, ss783571870, ss1337188117, ss1584067731, ss1624447275, ss1667441308, ss1689879703, ss1711254896, ss1751968430, ss1917846292, ss1946280886, ss1959257000, ss2337249696, ss2738210090, ss2748376498, ss2888038693, ss3006360783, ss3021234231, ss3626433939 NC_000010.10:43613907:A>T NC_000010.11:43118459:A>T (self)
RCV000014962.26, RCV000014963.29, RCV000021851.2, RCV000034771.5, RCV000123309.8, RCV000130367.4, RCV000148769.1, RCV000312825.1, RCV000370653.1, RCV000400976.1, RCV000419149.1, RCV000426589.1, RCV000431156.1, RCV000436831.1, RCV000441584.1, 41325788, ss157383340, ss275515845, ss2174314930, ss3118052380 NC_000010.11:43118459:A>T NC_000010.11:43118459: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.

14 citations for rs77724903
PMID Title Author Year Journal
9506724 A new hot spot for mutations in the ret protooncogene causing familial medullary thyroid carcinoma and multiple endocrine neoplasia type 2A. Berndt I et al. 1998 The Journal of clinical endocrinology and metabolism
12000816 Germ-line mutations in nonsyndromic pheochromocytoma. Neumann HP et al. 2002 The New England journal of medicine
15531714 Screening of six risk exons of the RET proto-oncogene in families with medullary thyroid carcinoma in the Czech Republic. Jindrichov√° S et al. 2004 The Journal of endocrinology
15753368 RET-familial medullary thyroid carcinoma mutants Y791F and S891A activate a Src/JAK/STAT3 pathway, independent of glial cell line-derived neurotrophic factor. Plaza Menacho I et al. 2005 Cancer research
15870131 Coincidence of multiple endocrine neoplasia types 1 and 2: mutations in the RET protooncogene and MEN1 tumor suppressor gene in a family presenting with recurrent primary hyperparathyroidism. Frank-Raue K et al. 2005 The Journal of clinical endocrinology and metabolism
16118333 Polymorphisms in exon 13 and intron 14 of the RET protooncogene: genetic modifiers of medullary thyroid carcinoma? Baumgartner-Parzer SM et al. 2005 The Journal of clinical endocrinology and metabolism
16705552 Double germline mutations in the RET Proto-oncogene in MEN 2A and MEN 2B kindreds. Dvorakova S et al. 2006 Experimental and clinical endocrinology & diabetes
19826964 RET mutation Tyr791Phe: the genetic cause of different diseases derived from neural crest. Vaclavikova E et al. 2009 Endocrine
19906784 Pathogenicity of DNA variants and double mutations in multiple endocrine neoplasia type 2 and von Hippel-Lindau syndrome. Erlic Z et al. 2010 The Journal of clinical endocrinology and metabolism
20080836 High penetrance of pheochromocytoma associated with the novel C634Y/Y791F double germline mutation in the RET protooncogene. Toledo RA et al. 2010 The Journal of clinical endocrinology and metabolism
22703879 Secondary variants in individuals undergoing exome sequencing: screening of 572 individuals identifies high-penetrance mutations in cancer-susceptibility genes. Johnston JJ et al. 2012 American journal of human genetics
25333069 Disease variants in genomes of 44 centenarians. Freudenberg-Hua Y et al. 2014 Molecular genetics & genomic medicine
25425582 Comprehensive assessment of the disputed RET Y791F variant shows no association with medullary thyroid carcinoma susceptibility. Toledo RA et al. 2015 Endocrine-related cancer
25741868 Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Richards S et al. 2015 Genetics in medicine

Genomic regions, transcripts, and products
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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: 0.1.4.post833+d3ba21e