16-89920053-C-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_002386.4(MC1R):c.795C>T(p.Val265=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000341 in 1,613,878 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 (★). Synonymous variant affecting the same amino acid position (i.e. V265V) has been classified as Likely benign.
Frequency
Consequence
NM_002386.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MC1R | NM_002386.4 | c.795C>T | p.Val265= | synonymous_variant | 1/1 | ENST00000555147.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MC1R | ENST00000555147.2 | c.795C>T | p.Val265= | synonymous_variant | 1/1 | NM_002386.4 | P1 | ||
ENST00000554623.1 | n.759G>A | non_coding_transcript_exon_variant | 2/2 | 3 | |||||
MC1R | ENST00000555427.1 | c.795C>T | p.Val265= | synonymous_variant | 3/4 | 5 | |||
MC1R | ENST00000639847.1 | c.795C>T | p.Val265= | synonymous_variant | 3/3 | 5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152234Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000100 AC: 25AN: 249200Hom.: 0 AF XY: 0.0000740 AC XY: 10AN XY: 135212
GnomAD4 exome AF: 0.0000315 AC: 46AN: 1461526Hom.: 0 Cov.: 35 AF XY: 0.0000303 AC XY: 22AN XY: 727024
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152352Hom.: 0 Cov.: 33 AF XY: 0.0000671 AC XY: 5AN XY: 74500
ClinVar
Submissions by phenotype
Melanoma, cutaneous malignant, susceptibility to, 5 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 30, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at