rs1057520515
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_000430.4(PAFAH1B1):c.1159+1G>A variant causes a splice donor, intron change involving the alteration of a 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 predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★★).
Frequency
Consequence
NM_000430.4 splice_donor, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 18 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 30
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Lissencephaly due to LIS1 mutation Pathogenic:1
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not provided Pathogenic:1
The c.1159+1 G>A splice site variant in the PAFAH1B1 gene destroys the canonical splice donor site inintron 10. It is predicted to cause abnormal gene splicing, either leading to an abnormal message that is subjectto nonsense-mediated mRNA decay, or to an abnormal protein product if the message is used for proteintranslation. Although this variant has not been previously reported to our knowledge, however we consider it to be a pathogenic variant. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at