rs142546324
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM2PM5PP2PP3_Strong
The NM_002474.3(MYH11):c.5273G>T(p.Arg1758Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000124 in 1,609,080 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1758Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_002474.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYH11 | NM_002474.3 | c.5273G>T | p.Arg1758Leu | missense_variant | 37/41 | ENST00000300036.6 | |
MYH11 | NM_001040113.2 | c.5294G>T | p.Arg1765Leu | missense_variant | 38/43 | ENST00000452625.7 | |
NDE1 | NM_017668.3 | c.948-5854C>A | intron_variant | ENST00000396354.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYH11 | ENST00000300036.6 | c.5273G>T | p.Arg1758Leu | missense_variant | 37/41 | 1 | NM_002474.3 | P3 | |
MYH11 | ENST00000452625.7 | c.5294G>T | p.Arg1765Leu | missense_variant | 38/43 | 1 | NM_001040113.2 | ||
NDE1 | ENST00000396354.6 | c.948-5854C>A | intron_variant | 1 | NM_017668.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152166Hom.: 0 Cov.: 32
GnomAD4 exome AF: 6.86e-7 AC: 1AN: 1456914Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 724904
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152166Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74334
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at