chr16-89917888-C-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The XM_047435031.1(LOC124903759):āc.1053C>Gā(p.Val351Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000307 in 211,494 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Consequence
XM_047435031.1 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MC1R | ENST00000555427 | c.-568C>G | 5_prime_UTR_variant | Exon 2 of 4 | 5 | ENSP00000451760.1 | ||||
MC1R | ENST00000639847 | c.-568C>G | 5_prime_UTR_variant | Exon 2 of 3 | 5 | ENSP00000492011.1 | ||||
ENSG00000267048 | ENST00000570217.1 | n.214C>G | non_coding_transcript_exon_variant | Exon 3 of 3 | 4 |
Frequencies
GnomAD3 genomes AF: 0.000243 AC: 37AN: 152244Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.000474 AC: 28AN: 59132Hom.: 0 Cov.: 0 AF XY: 0.000400 AC XY: 11AN XY: 27470
GnomAD4 genome AF: 0.000243 AC: 37AN: 152362Hom.: 0 Cov.: 33 AF XY: 0.000228 AC XY: 17AN XY: 74500
ClinVar
Submissions by phenotype
Melanoma, cutaneous malignant, susceptibility to, 5 Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at