rs200450661
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_005379.4(MYO1A):c.1928G>A(p.Arg643Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000403 in 1,614,152 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_005379.4 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 |
---|---|---|---|---|---|---|---|
MYO1A | NM_005379.4 | c.1928G>A | p.Arg643Gln | missense_variant | 18/28 | ENST00000300119.8 | |
MYO1A | NM_001256041.2 | c.1928G>A | p.Arg643Gln | missense_variant | 19/29 | ||
MYO1A | XM_047428876.1 | c.1928G>A | p.Arg643Gln | missense_variant | 19/29 | ||
MYO1A | XM_011538373.3 | c.1928G>A | p.Arg643Gln | missense_variant | 18/25 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYO1A | ENST00000300119.8 | c.1928G>A | p.Arg643Gln | missense_variant | 18/28 | 1 | NM_005379.4 | P1 | |
MYO1A | ENST00000442789.6 | c.1928G>A | p.Arg643Gln | missense_variant | 19/29 | 1 | P1 | ||
MYO1A | ENST00000554234.5 | c.1442G>A | p.Arg481Gln | missense_variant, NMD_transcript_variant | 14/24 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152172Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000319 AC: 8AN: 250974Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135660
GnomAD4 exome AF: 0.0000397 AC: 58AN: 1461862Hom.: 0 Cov.: 33 AF XY: 0.0000371 AC XY: 27AN XY: 727228
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152290Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74460
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Nov 18, 2014 | p.Arg643Gln in exon 18 of MYO1A: This variant is not expected to have clinical significance because the arginine (Arg) residue at position 643 is not conserved in mammals or across species, with guinea pig and rabbit having a glutamine (Gl n). In addition, recent evidence has disqualified an association between variant s in the MYO1A gene and hearing loss (Eisenberger 2014). This variant has also been identified in 0.5% (1/192) of Kenyan chromosomes by the 1000 Genomes Projec t (rs200450661). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at