chr3-69879359-G-A
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1
The NM_001354604.2(MITF):c.330G>A(p.Thr110Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00317 in 1,614,174 control chromosomes in the GnomAD database, including 132 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001354604.2 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MITF | NM_001354604.2 | c.330G>A | p.Thr110Thr | synonymous_variant | Exon 2 of 10 | ENST00000352241.9 | NP_001341533.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0158 AC: 2397AN: 152178Hom.: 58 Cov.: 32
GnomAD3 exomes AF: 0.00448 AC: 1115AN: 248830Hom.: 36 AF XY: 0.00359 AC XY: 485AN XY: 135032
GnomAD4 exome AF: 0.00183 AC: 2682AN: 1461878Hom.: 63 Cov.: 31 AF XY: 0.00162 AC XY: 1175AN XY: 727240
GnomAD4 genome AF: 0.0160 AC: 2439AN: 152296Hom.: 69 Cov.: 32 AF XY: 0.0160 AC XY: 1189AN XY: 74486
ClinVar
Submissions by phenotype
not provided Benign:4
- -
- -
- -
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. -
not specified Benign:2
Thr110Thr in exon 2 of MITF: This variant is not expected to have clinical signi ficance because it does not alter an amino acid residue and is not located withi n the splice consensus sequence. It has been identified in 4.8% (205/4268) of Af rican American chromosomes from a broad population by the NHLBI Exome Sequencing Project (http://evs.gs.washington.edu/EVS; dbSNP rs9849776). -
- -
MITF-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Melanoma, cutaneous malignant, susceptibility to, 8 Benign:1
- -
Waardenburg syndrome type 2A Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at