NM_000551.4(VHL):c.463+8C>T AND Hereditary cancer-predisposing syndrome

Germline classification:: Benign/Likely benign (3 submissions)
Last evaluated:: Aug 5, 2021
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000210772.11

Allele description [Variation Report for NM_000551.4(VHL):c.463+8C>T]

NM_000551.4(VHL):c.463+8C>T

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.463+8C>T

Other names:

IVS2+8C>T

HGVS:

NC_000003.12:g.10146644C>T
NG_008212.3:g.10010C>T
NG_046756.1:g.4406C>T
NM_000551.4:c.463+8C>TMANE SELECT
NM_001354723.2:c.*18-3143C>T
NM_198156.3:c.341-3143C>T
LRG_322t1:c.463+8C>T
LRG_322:g.10010C>T
NC_000003.11:g.10188328C>T
NM_000551.2:c.463+8C>T
NM_000551.3:c.463+8C>T

Links:

dbSNP: rs5030834

NCBI 1000 Genomes Browser:

rs5030834

Molecular consequence:

NM_000551.4:c.463+8C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001354723.2:c.*18-3143C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_198156.3:c.341-3143C>T - intron variant - [Sequence Ontology: SO:0001627]

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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RNA polymerase subunit 1 [African swine fever virus]
RNA polymerase subunit 1 [African swine fever virus]
gi|723633597|gb|AIY22448.1|

Protein
azo3556 AND (alive[prop]) (0)
Gene
lwe1904 AND (alive[prop]) (0)
Gene
azo0587 AND (alive[prop]) (0)
Gene
lwe2366 AND (alive[prop]) (0)
Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000267099	Vantari Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Feb 5, 2016)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002534176	Sema4, Sema4	criteria provided, single submitter (Sema4 Curation Guidelines)	Likely benign (Feb 21, 2021)	germline	curation	Citation Link,
SCV002636643	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Benign (Aug 5, 2021)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 11409863, 22799452, 9398721, 9663592 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000267099

Vantari Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely benign
(Feb 5, 2016)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV002534176

Sema4, Sema4

criteria provided, single submitter

(Sema4 Curation Guidelines)

Likely benign
(Feb 21, 2021)

germline

curation

Citation Link,

SCV002636643

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Benign
(Aug 5, 2021)

germline

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing, curation

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

DHPLC-based germline mutation screening in the analysis of the VHL tumor suppressor gene: usefulness and limitations.

Klein B, Weirich G, Brauch H.

Hum Genet. 2001 May;108(5):376-84.

PubMed [citation]

PMID:: 11409863

See all PubMed Citations (5)

Details of each submission

From Vantari Genetics, SCV000267099.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Sema4, Sema4, SCV002534176.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	curation	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Ambry Genetics, SCV002636643.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

This alteration is classified as 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.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Nov 3, 2024

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