VCV000677058.4 - ClinVar

NM_020975.6(RET):c.2608-147C>T

Germline

Classification

criteria provided, multiple submitters, no conflicts. Learn more about how ClinVar calculates review status.

Benign

2 out of 2 submissions contributed to this classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_020975.6(RET):c.2608-147C>T

Variation ID: 677058 Accession: VCV000677058.4

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 10q11.21 10: 43119934 (GRCh38) [ NCBI UCSC ] 10: 43615382 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Aug 26, 2019	Dec 17, 2022	Aug 6, 2019

HGVS

Nucleotide	Protein	Molecular consequence
NM_020975.6:c.2608-147C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.		intron variant
NM_001355216.2:c.1846-147C>T		intron variant
NM_001406743.1:c.2608-147C>T		intron variant
NM_001406744.1:c.2608-147C>T		intron variant
NM_001406759.1:c.2608-147C>T		intron variant
NM_001406760.1:c.2608-147C>T		intron variant
NM_001406761.1:c.2479-147C>T		intron variant
NM_001406762.1:c.2479-147C>T		intron variant
NM_001406763.1:c.2473-147C>T		intron variant
NM_001406764.1:c.2479-147C>T		intron variant
NM_001406765.1:c.2473-147C>T		intron variant
NM_001406766.1:c.2320-147C>T		intron variant
NM_001406767.1:c.2320-147C>T		intron variant
NM_001406768.1:c.2344-147C>T		intron variant
NM_001406769.1:c.2212-147C>T		intron variant
NM_001406770.1:c.2320-147C>T		intron variant
NM_001406771.1:c.2170-147C>T		intron variant
NM_001406772.1:c.2212-147C>T		intron variant
NM_001406773.1:c.2170-147C>T		intron variant
NM_001406774.1:c.2083-147C>T		intron variant
NM_001406775.1:c.1882-147C>T		intron variant
NM_001406776.1:c.1882-147C>T		intron variant
NM_001406777.1:c.1882-147C>T		intron variant
NM_001406778.1:c.1882-147C>T		intron variant
NM_001406779.1:c.1711-147C>T		intron variant
NM_001406780.1:c.1711-147C>T		intron variant
NM_001406781.1:c.1711-147C>T		intron variant
NM_001406782.1:c.1711-147C>T		intron variant
NM_001406783.1:c.1582-147C>T		intron variant
NM_001406784.1:c.1618-147C>T		intron variant
NM_001406785.1:c.1591-147C>T		intron variant
NM_001406786.1:c.1582-147C>T		intron variant
NM_001406787.1:c.1576-147C>T		intron variant
NM_001406788.1:c.1423-147C>T		intron variant
NM_001406789.1:c.1423-147C>T		intron variant
NM_001406790.1:c.1423-147C>T		intron variant
NM_001406791.1:c.1303-147C>T		intron variant
NM_001406792.1:c.1159-147C>T		intron variant
NM_001406793.1:c.1159-147C>T		intron variant
NM_001406794.1:c.1159-147C>T		intron variant
NM_020630.7:c.2608-147C>T		intron variant
NC_000010.11:g.43119934C>T
NC_000010.10:g.43615382C>T
NG_007489.1:g.47866C>T
LRG_518:g.47866C>T
LRG_518t1:c.2608-147C>T

... more HGVS ... less HGVS

Protein change

Other names

Canonical SPDI

NC_000010.11:43119933:C:T

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

0.17173 (T)

Allele frequency Help The frequency of the allele represented by this VCV record.

The Genome Aggregation Database (gnomAD) 0.17019

1000 Genomes Project 0.17173

The Genome Aggregation Database (gnomAD) 0.17296

1000 Genomes Project 30x 0.17333

Trans-Omics for Precision Medicine (TOPMed) 0.17339

Links

ClinGen: CA13264953 dbSNP: rs11238441 VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
RET		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	4106	4237

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
not provided	Benign (1)	criteria provided, single submitter	Jun 20, 2018	RCV000836540.3
Multiple endocrine neoplasia, type 2	Benign (1)	criteria provided, single submitter	Aug 6, 2019	RCV002466593.1

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	Expand all rows Collapse all rows Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Benign (Jun 20, 2018) C Contributing to aggregate classification	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Not Provided	GeneDx Accession: SCV000978385.1 First in ClinVar: Aug 26, 2019 Last updated: Aug 26, 2019	Comment: show This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. (less) Observation: 1 Collection method: clinical testing Allele origin: germline Affected status: yes Observation 1 Collection method: clinical testing Allele origin: germline Affected status: yes

Benign (Aug 06, 2019) C Contributing to aggregate classification	criteria provided, single submitter (ACMG Guidelines, 2015)	Multiple endocrine neoplasia, type 2 (Autosomal dominant inheritance)	Genetics and Molecular Pathology, SA Pathology Additional submitter: Shariant Australia, Australian Genomics Accession: SCV002761366.1 First in ClinVar: Dec 17, 2022 Last updated: Dec 17, 2022	Observation: 1 Collection method: clinical testing Allele origin: germline Affected status: yes Observation 1 Collection method: clinical testing Allele origin: germline Affected status: yes

Comment:

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

Citations for germline classification of this variant

There are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs11238441 ...

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 May 17, 2025

ClinVar Genomic variation as it relates to human health

NM_020975.6(RET):c.2608-147C>T

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Citations for germline classification of this variant

Text-mined citations for rs11238441 ...