chr6-75890063-A-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBP6
The NM_004999.4(MYO6):āc.2665A>Gā(p.Met889Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000254 in 1,611,422 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_004999.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152202Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 250426Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135640
GnomAD4 exome AF: 0.0000151 AC: 22AN: 1459220Hom.: 0 Cov.: 31 AF XY: 0.0000165 AC XY: 12AN XY: 726114
GnomAD4 genome AF: 0.000125 AC: 19AN: 152202Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74368
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Nov 15, 2023 | In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | May 01, 2014 | Met889Val in exon 26 of MYO6: This variant is not expected to have clinical sign ificance due to a lack of conservation across species, including mammals. Of not e, at least 3 mammals (alpaca, Bactrian camel, and platypus) have a valine (Val) at this position despite high nearby amino acid conservation. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at