NM_000245.4(MET):c.1715G>A (p.Ser572Asn) AND Hereditary cancer-predisposing syndrome

Germline classification:: Likely benign (2 submissions)
Last evaluated:: Apr 23, 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:: RCV000564000.4

Allele description [Variation Report for NM_000245.4(MET):c.1715G>A (p.Ser572Asn)]

NM_000245.4(MET):c.1715G>A (p.Ser572Asn)

Gene:

MET:MET proto-oncogene, receptor tyrosine kinase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

7q31.2

Genomic location:

Preferred name:

NM_000245.4(MET):c.1715G>A (p.Ser572Asn)

HGVS:

NC_000007.14:g.116755368G>A
NG_008996.1:g.87964G>A
NM_000245.4:c.1715G>AMANE SELECT
NM_001127500.3:c.1715G>A
NM_001324401.3:c.1715G>A
NM_001324402.2:c.425G>A
NP_000236.2:p.Ser572Asn
NP_001120972.1:p.Ser572Asn
NP_001311330.1:p.Ser572Asn
NP_001311331.1:p.Ser142Asn
LRG_662t1:c.1715G>A
LRG_662:g.87964G>A
NC_000007.13:g.116395422G>A
NM_001127500.1:c.1715G>A
NM_001127500.2:c.1715G>A

Protein change:

S142N

Links:

dbSNP: rs199771406

NCBI 1000 Genomes Browser:

rs199771406

Molecular consequence:

NM_000245.4:c.1715G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001127500.3:c.1715G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001324401.3:c.1715G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001324402.2:c.425G>A - missense variant - [Sequence Ontology: SO:0001583]

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000664651	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Likely benign (Jun 20, 2018)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link,
SCV002532109	Sema4, Sema4	criteria provided, single submitter (Sema4 Curation Guidelines)	Likely benign (Apr 23, 2021)	germline	curation	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000664651

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Likely benign
(Jun 20, 2018)

germline

clinical testing

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

Citation Link,

SCV002532109

Sema4, Sema4

criteria provided, single submitter

(Sema4 Curation Guidelines)

Likely benign
(Apr 23, 2021)

germline

curation

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

REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants.

Ioannidis NM, Rothstein JH, Pejaver V, Middha S, McDonnell SK, Baheti S, Musolf A, Li Q, Holzinger E, Karyadi D, Cannon-Albright LA, Teerlink CC, Stanford JL, Isaacs WB, Xu J, Cooney KA, Lange EM, Schleutker J, Carpten JD, Powell IJ, Cussenot O, Cancel-Tassin G, et al.

Am J Hum Genet. 2016 Oct 6;99(4):877-885. doi: 10.1016/j.ajhg.2016.08.016. Epub 2016 Sep 22.

PubMed [citation]

PMID:: 27666373
PMCID:: PMC5065685

Details of each submission

From Ambry Genetics, SCV000664651.5

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

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.

#	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, SCV002532109.1

#	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

Last Updated: Oct 13, 2024

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