chr15-57621638-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP5
The NM_001018100.5(MYZAP):c.349C>T(p.Arg117Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000151 in 1,461,390 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_001018100.5 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYZAP | NM_001018100.5 | c.349C>T | p.Arg117Ter | stop_gained | 4/13 | ENST00000267853.10 | |
GCOM1 | NR_104367.2 | n.480C>T | non_coding_transcript_exon_variant | 4/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYZAP | ENST00000267853.10 | c.349C>T | p.Arg117Ter | stop_gained | 4/13 | 1 | NM_001018100.5 | P1 | |
MYZAP | ENST00000380565.8 | c.349C>T | p.Arg117Ter | stop_gained | 4/12 | 1 | |||
GCOM1 | ENST00000649429.1 | c.349C>T | p.Arg117Ter | stop_gained | 4/11 | ||||
MYZAP | ENST00000569089.1 | c.304C>T | p.Arg102Ter | stop_gained | 5/6 | 4 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251088Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135692
GnomAD4 exome AF: 0.0000151 AC: 22AN: 1461390Hom.: 0 Cov.: 30 AF XY: 0.0000151 AC XY: 11AN XY: 726980
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
CARDIOMYOPATHY, DILATED, 2K Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jul 15, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at