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NM_020975.6(RET):c.3188-9C>T

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(4);Likely benign(3);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
9 (Most recent: Jan 7, 2021)
Last evaluated:
Nov 1, 2020
Accession:
VCV000136116.5
Variation ID:
136116
Description:
single nucleotide variant
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NM_020975.6(RET):c.3188-9C>T

Allele ID
139828
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
10q11.21
Genomic location
10: 43128103 (GRCh38) GRCh38 UCSC
10: 43623551 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000010.10:g.43623551C>T
NC_000010.11:g.43128103C>T
NM_020975.6:c.3188-9C>T MANE Select
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000010.11:43128102:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00040 (T)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00041
1000 Genomes Project 0.00040
Exome Aggregation Consortium (ExAC) 0.00051
The Genome Aggregation Database (gnomAD) 0.00003
Trans-Omics for Precision Medicine (TOPMed) 0.00003
Links
ClinGen: CA010891
dbSNP: rs551159582
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 1 criteria provided, single submitter Nov 1, 2020 RCV000123318.7
Uncertain significance 1 criteria provided, single submitter Dec 10, 2015 RCV000410823.1
Likely benign 1 criteria provided, single submitter Jul 5, 2017 RCV000597670.2
Likely benign 1 criteria provided, single submitter Jan 13, 2018 RCV001108240.1
Benign 1 criteria provided, single submitter Jan 13, 2018 RCV001108241.1
Benign 1 criteria provided, single submitter Jan 13, 2018 RCV001108242.1
Likely benign 1 criteria provided, single submitter Jan 13, 2018 RCV001108243.1
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Jul 2, 2018 RCV000412312.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
RET Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
1785 1880

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Jul 02, 2018)
criteria provided, single submitter
Method: clinical testing
Multiple endocrine neoplasia, type 2a
Allele origin: unknown
Mendelics
Accession: SCV000838410.1
Submitted: (Aug 20, 2018)
Evidence details
Benign
(Nov 01, 2020)
criteria provided, single submitter
Method: clinical testing
Multiple endocrine neoplasia, type 2
Allele origin: germline
Invitae
Accession: SCV000166625.7
Submitted: (Jan 07, 2021)
Evidence details
Uncertain significance
(Dec 10, 2015)
criteria provided, single submitter
Method: clinical testing
Multiple endocrine neoplasia, type 2b
Allele origin: unknown
Counsyl
Accession: SCV000489765.1
Submitted: (Nov 23, 2016)
Evidence details
Publications
PubMed (1)
Uncertain significance
(Dec 10, 2015)
criteria provided, single submitter
Method: clinical testing
Multiple endocrine neoplasia, type 2a
Allele origin: unknown
Counsyl
Accession: SCV000489766.1
Submitted: (Nov 23, 2016)
Evidence details
Publications
PubMed (1)
Likely benign
(Jul 05, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000700633.2
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Likely benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Hirschsprung disease 1
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001265454.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Multiple endocrine neoplasia
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001265455.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Pheochromocytoma
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001265456.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Likely benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Renal hypodysplasia/aplasia 1
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001265457.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Novel RET mutations in Hirschsprung's disease patients from the diverse South African population. Julies MG European journal of human genetics : EJHG 2001 PMID: 11436122
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=RET - - - -

Text-mined citations for rs551159582...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Jun 14, 2021