16-89920053-C-G
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_002386.4(MC1R):āc.795C>Gā(p.Val265=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000582 in 1,613,876 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. V265V) has been classified as Benign.
Frequency
Consequence
NM_002386.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MC1R | NM_002386.4 | c.795C>G | 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>G | p.Val265= | synonymous_variant | 1/1 | NM_002386.4 | P1 | ||
ENST00000554623.1 | n.759G>C | non_coding_transcript_exon_variant | 2/2 | 3 | |||||
MC1R | ENST00000555427.1 | c.795C>G | p.Val265= | synonymous_variant | 3/4 | 5 | |||
MC1R | ENST00000639847.1 | c.795C>G | p.Val265= | synonymous_variant | 3/3 | 5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000243 AC: 37AN: 152232Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000682 AC: 17AN: 249200Hom.: 0 AF XY: 0.0000444 AC XY: 6AN XY: 135212
GnomAD4 exome AF: 0.0000356 AC: 52AN: 1461526Hom.: 1 Cov.: 35 AF XY: 0.0000344 AC XY: 25AN XY: 727024
GnomAD4 genome AF: 0.000276 AC: 42AN: 152350Hom.: 0 Cov.: 33 AF XY: 0.000349 AC XY: 26AN XY: 74498
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Melanoma, cutaneous malignant, susceptibility to, 5 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2023 | - - |
Tyrosinase-positive oculocutaneous albinism;C1849452:Skin/hair/eye pigmentation, variation in, 2;C2751295:Melanoma, cutaneous malignant, susceptibility to, 5;C2751296:Increased analgesia from kappa-opioid receptor agonist, female-specific Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | May 24, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at