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NM_000551.4(VHL):c.417T>G (p.Ser139=) AND Hereditary cancer-predisposing syndrome

Germline classification:
Likely benign (1 submission)
Last evaluated:
Apr 13, 2020
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV002331801.2

Allele description [Variation Report for NM_000551.4(VHL):c.417T>G (p.Ser139=)]

NM_000551.4(VHL):c.417T>G (p.Ser139=)

Genes:
LOC107303340:3p25 von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase Alu-mediated recombination region [Gene]
VHL:von Hippel-Lindau tumor suppressor [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
3p25.3
Genomic location:
Preferred name:
NM_000551.4(VHL):c.417T>G (p.Ser139=)
HGVS:
  • NC_000003.12:g.10146590T>G
  • NG_008212.3:g.9956T>G
  • NG_046756.1:g.4352T>G
  • NM_000551.4:c.417T>GMANE SELECT
  • NM_001354723.2:c.*18-3197T>G
  • NM_198156.3:c.341-3197T>G
  • NP_000542.1:p.Ser139=
  • LRG_322t1:c.417T>G
  • LRG_322:g.9956T>G
  • NC_000003.11:g.10188274T>G
  • NM_000551.3:c.417T>G
Links:
dbSNP: rs1406004337
NCBI 1000 Genomes Browser:
rs1406004337
Molecular consequence:
  • NM_001354723.2:c.*18-3197T>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_198156.3:c.341-3197T>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000551.4:c.417T>G - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:
Hereditary cancer-predisposing syndrome
Synonyms:
Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002629446Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Likely benign
(Apr 13, 2020) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Ambry Genetics, SCV002629446.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024