chr9-21974641-C-G
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM1BP6BS1BS2
The NM_058197.5(CDKN2A):āc.187G>Cā(p.Gly63Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00262 in 1,614,214 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_058197.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00202 AC: 308AN: 152228Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00202 AC: 507AN: 250906Hom.: 1 AF XY: 0.00213 AC XY: 289AN XY: 135654
GnomAD4 exome AF: 0.00268 AC: 3921AN: 1461868Hom.: 7 Cov.: 32 AF XY: 0.00273 AC XY: 1984AN XY: 727240
GnomAD4 genome AF: 0.00202 AC: 308AN: 152346Hom.: 0 Cov.: 32 AF XY: 0.00199 AC XY: 148AN XY: 74502
ClinVar
Submissions by phenotype
not provided Uncertain:2Benign:7
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CDKN2A: BS1, BS2 -
not specified Uncertain:2Benign:1Other:1
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Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Reported in a family with melanoma, segregated in 2 individuals with atypical naevi and 1 with melanoma (Balogh 2012). MAF 0.3%. -
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. -
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Melanoma-pancreatic cancer syndrome Uncertain:1Benign:2
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This variant is considered benign. This variant is intronic and is not expected to impact mRNA splicing. -
Hereditary cancer-predisposing syndrome Uncertain:1Benign:1
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The p.G63R variant (also known as c.187G>C), located in coding exon 1 of the CDKN2A gene, results from a G to C substitution at nucleotide position 187. The glycine at codon 63 is replaced by arginine, an amino acid with dissimilar properties. A 47 year old male patient with malignant melanoma at age 43, from an Italian melanoma family, was reported to have this variant; this individual did not have the pathogenic CDKN2A p.R24P mutation that was present in other family members (Della Torre G et al. Br. J. Cancer. 2001 Sep;85:836-44). This variant has been reported in individuals with single primary melanoma and with multiple primary melanomas (Goldstein AM et al. J. Med. Genet. 2008 May;45:284-9; Pastorino L et al. Pigment Cell Melanoma Res. 2008 Dec;21:700-9; Bruno W et al. J. Am. Acad. Dermatol. 2016 Feb;74:325-32). However, in other studies this variant has been reported in both melanoma cases controls (Harland M et al. Hered Cancer Clin Pract. 2014 Nov;12:20). Using a minigene assay to investigate mRNA splicing regulation, this variant had a differential splicing pattern from wild-type (Balogh K et al. Br. J. Dermatol. 2012 Jul;167:131-3). This variant has also been reported in studies of patients with pancreatic cancer (Ghiorzo P et al. J. Med. Genet. 2012 Mar;49:164-70; Grant RC et al. Gastroenterology. 2015 Mar;148:556-64). It was also identified in a cohort of 681 ancestrally diverse, healthy subjects (Bodian DL et al. PLoS ONE. 2014 Apr;9:e94554); and it was detected as a secondary finding in 4 out of 567 ClinSeq participants, unselected for personal or family history of cancer, who underwent exome sequencing (Johnston JJ et al. Am. J. Hum. Genet. 2012 Jul;91:97-108). This amino acid position is poorly conserved in available vertebrate species. Of note, this alteration is also designated as c.150+37G>C and IVS150+37G>C in the published literature. Since supporting evidence is conflicting at this time, the clinical significance of this alteration remains unclear. -
CDKN2A-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Familial melanoma Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at