NM_002386.4(MC1R):c.586T>C (p.Phe196Leu) AND Melanoma, cutaneous malignant, susceptibility to, 5

Germline classification:: Benign/Likely benign (2 submissions)
Last evaluated:: Jan 19, 2024
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:: RCV000461696.16

Allele description [Variation Report for NM_002386.4(MC1R):c.586T>C (p.Phe196Leu)]

NM_002386.4(MC1R):c.586T>C (p.Phe196Leu)

Gene:

MC1R:melanocortin 1 receptor [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

16q24.3

Genomic location:

Preferred name:

NM_002386.4(MC1R):c.586T>C (p.Phe196Leu)

HGVS:

NC_000016.10:g.89919844T>C
NG_012026.1:g.6966T>C
NG_027810.1:g.2836T>C
NM_002386.4:c.586T>CMANE SELECT
NP_002377.4:p.Phe196Leu
NP_002377.4:p.Phe196Leu
NC_000016.9:g.89986252T>C
NM_002386.3:c.586T>C
Q01726:p.Phe196Leu

Protein change:

F196L

Links:

UniProtKB: Q01726#VAR_013616; dbSNP: rs3212366

NCBI 1000 Genomes Browser:

rs3212366

Molecular consequence:

NM_002386.4:c.586T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Melanoma, cutaneous malignant, susceptibility to, 5
Synonyms:: Cutaneous malignant melanoma 5
Identifiers:: MONDO: MONDO:0013133; MedGen: C2751295; Orphanet: 618; OMIM: 613099

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000399965	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Likely benign (Apr 27, 2017)	germline	clinical testing	PubMed (9) [See all records that cite these PMIDs] 16988943, 12851329, 23647022, 20876876, 16595073, 18402696, 22547573, 16280005, 15979202 Citation Link,
SCV000556938	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Benign (Jan 19, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000399965

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Likely benign
(Apr 27, 2017)

germline

clinical testing

PubMed (9)
[See all records that cite these PMIDs]

Citation Link,

SCV000556938

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Benign
(Jan 19, 2024)

germline

clinical testing

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

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

Citations

PubMed

MC1R common variants, CDKN2A and their association with melanoma and breast cancer risk.

Debniak T, Scott R, Masojc B, Serrano-Fernández P, Huzarski T, Byrski T, Debniak B, Górski B, Cybulski C, Medrek K, Kurzawski G, van de Wetering T, Maleszka R, Kładny J, Lubinski J.

Int J Cancer. 2006 Dec 1;119(11):2597-602.

PubMed [citation]

PMID:: 16988943

DNA polymorphism and selection at the melanocortin-1 receptor gene in normally pigmented southern African individuals.

John PR, Makova K, Li WH, Jenkins T, Ramsay M.

Ann N Y Acad Sci. 2003 Jun;994:299-306.

PubMed [citation]

PMID:: 12851329

See all PubMed Citations (10)

Details of each submission

From Illumina Laboratory Services, Illumina, SCV000399965.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (9)

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.

#	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 Labcorp Genetics (formerly Invitae), Labcorp, SCV000556938.9

#	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

Last Updated: Oct 20, 2024

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