rs200048542
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001080779.2(MYO1C):c.391C>T(p.Arg131Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000378 in 1,611,726 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R131H) has been classified as Uncertain significance.
Frequency
Consequence
NM_001080779.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYO1C | NM_001080779.2 | c.391C>T | p.Arg131Cys | missense_variant | 4/32 | ENST00000648651.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYO1C | ENST00000648651.1 | c.391C>T | p.Arg131Cys | missense_variant | 4/32 | NM_001080779.2 |
Frequencies
GnomAD3 genomes AF: 0.000441 AC: 67AN: 152032Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000473 AC: 117AN: 247110Hom.: 0 AF XY: 0.000566 AC XY: 76AN XY: 134286
GnomAD4 exome AF: 0.000372 AC: 543AN: 1459694Hom.: 1 Cov.: 39 AF XY: 0.000369 AC XY: 268AN XY: 726200
GnomAD4 genome AF: 0.000441 AC: 67AN: 152032Hom.: 0 Cov.: 31 AF XY: 0.000566 AC XY: 42AN XY: 74260
ClinVar
Submissions by phenotype
Anophthalmia-microphthalmia syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Paul Sabatier University EA-4555, Paul Sabatier University | Jan 01, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at