chr10:43615094:C>T Detail (hg19) (RET)

Information

Genome

Assembly Position
hg19 chr10:43,615,094-43,615,094
hg38 chr10:43,119,646-43,119,646 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_020975.4:c.2508C>T NP_066124.1:p.Ser836=
NM_020630.4:c.2508C>T NP_065681.1:p.Ser836=
Ensemble ENST00000355710.8:c.2508C>T ENST00000355710.8:p.Ser836=
Summary

MGeND

Clinical significance Likely benign
Variant entry 11
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.002
ToMMo:<0.001
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.002

Prediction

ClinVar

Clinical Significance Benign Likely benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 164761 OMIM
HGNC 9967 HGNC
Ensembl ENSG00000165731 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv39098385 TogoVar
COSMIC COSM6493955 COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Likely benign 2020/04/20 body of stomach not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
Likely benign 2020/04/20 stomach, unspecified not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
Likely benign 2020/04/20 caecum not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
Likely benign 2020/04/20 descending colon not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
Likely benign 2020/04/20 malignant neoplasm of rectum not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
Likely benign 2020/04/20 intrahepatic bile duct carcinoma not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
Likely benign 2020/04/20 bronchus or lung, unspecified not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2023-08-15 criteria provided, multiple submitters, no conflicts not specified germline Detail
Benign Likely benign 2017-04-27 criteria provided, multiple submitters, no conflicts multiple endocrine neoplasia germline unknown Detail
Likely benign 2017-04-27 criteria provided, single submitter Hirschsprung disease, susceptibility to, 1 germline Detail
Likely benign 2017-04-27 criteria provided, single submitter pheochromocytoma germline Detail
Likely benign 2017-04-27 criteria provided, single submitter Renal hypodysplasia/aplasia 1 germline Detail
Benign 2020-12-18 criteria provided, multiple submitters, no conflicts not provided germline Detail
Benign 2019-05-07 criteria provided, single submitter Hereditary cancer-predisposing syndrome germline Detail
Benign 2024-02-01 criteria provided, multiple submitters, no conflicts Multiple endocrine neoplasia, type 2 germline Detail
Benign 2023-07-07 criteria provided, single submitter multiple endocrine neoplasia type 2B germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.003 Thyroid Nodule Elevated thyroid nodule risks were associated with the minor alleles of RET S836... BeFree 19138047 Detail
0.004 Thyroid Nodule Elevated thyroid nodule risks were associated with the minor alleles of RET S836... BeFree 19138047 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_020975.6(RET):c.2508C>T (p.Ser836=) AND not specified ClinVar Detail
NM_020975.6(RET):c.2508C>T (p.Ser836=) AND Multiple endocrine neoplasia ClinVar Detail
NM_020975.6(RET):c.2508C>T (p.Ser836=) AND Hirschsprung disease, susceptibility to, 1 ClinVar Detail
NM_020975.6(RET):c.2508C>T (p.Ser836=) AND Pheochromocytoma ClinVar Detail
NM_020975.6(RET):c.2508C>T (p.Ser836=) AND Renal hypodysplasia/aplasia 1 ClinVar Detail
NM_020975.6(RET):c.2508C>T (p.Ser836=) AND not provided ClinVar Detail
NM_020975.6(RET):c.2508C>T (p.Ser836=) AND Hereditary cancer-predisposing syndrome ClinVar Detail
NM_020975.6(RET):c.2508C>T (p.Ser836=) AND Multiple endocrine neoplasia, type 2 ClinVar Detail
NM_020975.6(RET):c.2508C>T (p.Ser836=) AND Multiple endocrine neoplasia type 2B ClinVar Detail
Elevated thyroid nodule risks were associated with the minor alleles of RET S836S (rs1800862, P = 0.... DisGeNET Detail
Elevated thyroid nodule risks were associated with the minor alleles of RET S836S (rs1800862, P = 0.... DisGeNET Detail

Overlapped Transcript Coordinates

Gene Transcript ID Exon Number Chromosome Start Stop Type Amino Mutation Transcript Position Links

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs1800862 dbSNP
Genome
hg19
Position
chr10:43,615,094-43,615,094
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
Filtering Status (HGVD)
LowQual
# of samples (HGVD)
1207
Mean of sample read depth (HGVD)
69.74
Standard deviation of sample read depth (HGVD)
35.47
Number of reference allele (HGVD)
2409
Number of alternative allele (HGVD)
5
Allele Frequency (HGVD)
0.002071251035625518
Gene Symbol (HGVD)
RET
ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
PASS
Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
rs1800862
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0007
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
12
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8546
East Asian Allele Counts (ExAC)
13
East Asian Heterozygous Counts (ExAC)
13
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
0.0015211794991809033
Chromosome Counts in All Race (ExAC)
118460
Allele Counts in All Race (ExAC)
5527
Heterozygous Counts in All Race (ExAC)
5151
Homozygous Counts in All Race (ExAC)
188
Allele Frequency in All Race (ExAC)
0.04665709944284991
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