rs1129406
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_005171.5(ATF1):c.327C>A(p.Tyr109*) variant causes a stop gained, splice region change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_005171.5 stop_gained, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ATF1 | ENST00000262053.8 | c.327C>A | p.Tyr109* | stop_gained, splice_region_variant | Exon 4 of 7 | 1 | NM_005171.5 | ENSP00000262053.3 | ||
ATF1 | ENST00000552487.1 | c.327C>A | p.Tyr109* | stop_gained, splice_region_variant | Exon 4 of 6 | 5 | ENSP00000448921.1 | |||
ATF1 | ENST00000552510.5 | c.327C>A | p.Tyr109* | stop_gained, splice_region_variant | Exon 4 of 5 | 5 | ENSP00000448592.1 | |||
ATF1 | ENST00000551831.5 | n.94-4422C>A | intron_variant | Intron 3 of 5 | 2 | ENSP00000448987.1 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome Cov.: 37
GnomAD4 genome Cov.: 31
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at