rs61753238
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PVS1PM2
The NM_000288.4(PEX7):c.120C>A(p.Tyr40Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000835 in 1,198,062 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. Synonymous variant affecting the same amino acid position (i.e. Y40Y) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_000288.4 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PEX7 | NM_000288.4 | c.120C>A | p.Tyr40Ter | stop_gained | 1/10 | ENST00000318471.5 | |
PEX7 | XM_006715502.3 | c.120C>A | p.Tyr40Ter | stop_gained | 1/7 | ||
PEX7 | XM_047418874.1 | c.120C>A | p.Tyr40Ter | stop_gained | 1/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PEX7 | ENST00000318471.5 | c.120C>A | p.Tyr40Ter | stop_gained | 1/10 | 1 | NM_000288.4 | P1 | |
PEX7 | ENST00000367756.8 | c.120C>A | p.Tyr40Ter | stop_gained | 1/4 | 3 | |||
PEX7 | ENST00000541292.6 | c.120C>A | p.Tyr40Ter | stop_gained, NMD_transcript_variant | 1/11 | 5 | |||
PEX7 | ENST00000678593.1 | c.120C>A | p.Tyr40Ter | stop_gained, NMD_transcript_variant | 1/8 |
Frequencies
GnomAD3 genomes ? Cov.: 35
GnomAD3 exomes AF: 0.0000416 AC: 1AN: 24010Hom.: 0 AF XY: 0.0000655 AC XY: 1AN XY: 15258
GnomAD4 exome AF: 8.35e-7 AC: 1AN: 1198062Hom.: 0 Cov.: 32 AF XY: 0.00000171 AC XY: 1AN XY: 583098
GnomAD4 genome ? Cov.: 35
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at