chr10:43620335:C>T Detail (hg19) (RET)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr10:43,620,335-43,620,335 |
| hg38 | chr10:43,124,887-43,124,887 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_020630.4:c.2944C>T | NP_065681.1:p.Arg982Cys |
| NM_020975.4:c.2944C>T | NP_066124.1:p.Arg982Cys | |
| Ensemble | ENST00000713926.1:c.2680C>T | ENST00000713926.1:p.Arg894Cys |
Summary
MGeND
| Clinical significance |
Likely benign
|
| Variant entry | 30 |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.005 |
| ToMMo:0.003 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.013 |
Prediction
ClinVar
| Clinical Significance | Conflicting classifications of pathogenicity |
| Review star |  |
| Show details | |
Disease area statistics
MGeND
| Clinical significance | Last evaluated | Condition | Origin | Submission ID | Submitter | Institute | Citation | Comment | Image |
|---|---|---|---|---|---|---|---|---|---|
|
Likely benign
|
2020/04/20 | middle third of oesophagus |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | fundus of stomach |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | pyloric antrum |
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 | sigmoid colon |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | colon, unspecified |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | malignant neoplasm of rectosigmoid junction |
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 | extrahepatic bile duct |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | head of pancreas |
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 |
|---|---|---|---|---|---|
|
Likely benign
|
2017-04-27 | criteria provided, single submitter | Hirschsprung disease, susceptibility to, 1 |
germline
|
Detail |
Benign
|
2024-04-01 | criteria provided, multiple submitters, no conflicts | not provided |
germline
|
Detail |
|
Benign
|
2023-08-15 | criteria provided, multiple submitters, no conflicts | not specified |
germline
|
Detail |
|
Benign
|
2020-10-15 | criteria provided, multiple submitters, no conflicts | Hereditary cancer-predisposing syndrome |
germline
|
Detail |
|
Benign
Likely benign
|
2017-04-27 | criteria provided, multiple submitters, no conflicts | multiple endocrine neoplasia |
germline
unknown
|
Detail |
|
Benign
|
2015-09-24 | criteria provided, single submitter | familial medullary thyroid carcinoma |
unknown
|
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
|
2023-07-07 | criteria provided, multiple submitters, no conflicts | multiple endocrine neoplasia type 2B |
germline
unknown
|
Detail |
Conflicting interpretations of pathogenicity
|
2016-11-01 | criteria provided, conflicting interpretations | multiple endocrine neoplasia type 2A |
germline
unknown
|
Detail |
Uncertain significance
|
2013-01-01 | no assertion criteria provided | Aganglionic megacolon |
inherited
|
Detail |
|
Benign
|
2024-02-05 | criteria provided, multiple submitters, no conflicts | Multiple endocrine neoplasia, type 2 |
germline
|
Detail |
|
Benign
|
no assertion criteria provided |
germline
|
Detail | ||
|
Likely benign
|
2022-02-01 | criteria provided, single submitter | Breast-ovarian cancer, familial, susceptibility to, 1 |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.305 | multiple endocrine neoplasia | NA | CLINVAR | Detail | |
| 0.156 | Hirschsprung disease 1 | NA | CLINVAR | Detail | |
| 0.126 | Neoplastic Syndromes, Hereditary | NA | CLINVAR | Detail | |
| 0.362 | familial medullary thyroid carcinoma | The results confirmed the successful clinical utility of whole exome sequencing,... | BeFree | 21655256 | Detail |
| 0.522 | familial medullary thyroid carcinoma | The results confirmed the successful clinical utility of whole exome sequencing,... | BeFree | 21655256 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_020975.6(RET):c.2944C>T (p.Arg982Cys) AND Hirschsprung disease, susceptibility to, 1 | ClinVar | Detail |
| NM_020975.6(RET):c.2944C>T (p.Arg982Cys) AND not provided | ClinVar | Detail |
| NM_020975.6(RET):c.2944C>T (p.Arg982Cys) AND not specified | ClinVar | Detail |
| NM_020975.6(RET):c.2944C>T (p.Arg982Cys) AND Hereditary cancer-predisposing syndrome | ClinVar | Detail |
| NM_020975.6(RET):c.2944C>T (p.Arg982Cys) AND Multiple endocrine neoplasia | ClinVar | Detail |
| NM_020975.6(RET):c.2944C>T (p.Arg982Cys) AND Familial medullary thyroid carcinoma | ClinVar | Detail |
| NM_020975.6(RET):c.2944C>T (p.Arg982Cys) AND Pheochromocytoma | ClinVar | Detail |
| NM_020975.6(RET):c.2944C>T (p.Arg982Cys) AND Renal hypodysplasia/aplasia 1 | ClinVar | Detail |
| NM_020975.6(RET):c.2944C>T (p.Arg982Cys) AND Multiple endocrine neoplasia type 2B | ClinVar | Detail |
| NM_020975.6(RET):c.2944C>T (p.Arg982Cys) AND Multiple endocrine neoplasia type 2A | ClinVar | Detail |
| NM_020975.6(RET):c.2944C>T (p.Arg982Cys) AND Aganglionic megacolon | ClinVar | Detail |
| NM_020975.6(RET):c.2944C>T (p.Arg982Cys) AND Multiple endocrine neoplasia, type 2 | ClinVar | Detail |
| NM_020975.6(RET):c.2944C>T (p.Arg982Cys) AND Malignant tumor of breast | ClinVar | Detail |
| NM_020975.6(RET):c.2944C>T (p.Arg982Cys) AND Breast-ovarian cancer, familial, susceptibility to, 1 | ClinVar | Detail |
| NA | DisGeNET | Detail |
| NA | DisGeNET | Detail |
| NA | DisGeNET | Detail |
| The results confirmed the successful clinical utility of whole exome sequencing, and our data sugges... | DisGeNET | Detail |
| The results confirmed the successful clinical utility of whole exome sequencing, and our data sugges... | 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
- rs17158558 dbSNP
- Genome
- hg19
- Position
- chr10:43,620,335-43,620,335
- Variant Type
- snv
- Reference Allele
- C
- Alternative Allele
- T
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1044
- Mean of sample read depth (HGVD)
- 24.40
- Standard deviation of sample read depth (HGVD)
- 13.82
- Number of reference allele (HGVD)
- 2078
- Number of alternative allele (HGVD)
- 10
- Allele Frequency (HGVD)
- 0.004789272030651341
- 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))
- rs17158558
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.0027
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 45
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8654
- East Asian Allele Counts (ExAC)
- 110
- East Asian Heterozygous Counts (ExAC)
- 110
- East Asian Homozygous Counts (ExAC)
- 0
- East Asian Allele Frequency (ExAC)
- 0.012710885139819737
- Chromosome Counts in All Race (ExAC)
- 121372
- Allele Counts in All Race (ExAC)
- 2335
- Heterozygous Counts in All Race (ExAC)
- 2281
- Homozygous Counts in All Race (ExAC)
- 27
- Allele Frequency in All Race (ExAC)
- 0.019238374583923804
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