rs2031257693
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PVS1_StrongPM2
The NM_001171155.2(PET100):c.28-2A>C variant causes a splice acceptor, intron change. The variant allele was found at a frequency of 0.00000195 in 1,536,248 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001171155.2 splice_acceptor, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PET100 | NM_001171155.2 | c.28-2A>C | splice_acceptor_variant, intron_variant | Intron 1 of 3 | ENST00000594797.6 | NP_001164626.1 | ||
STXBP2 | NM_001414484.1 | c.-170-2A>C | splice_acceptor_variant, intron_variant | Intron 1 of 20 | NP_001401413.1 | |||
PET100 | NR_033242.2 | n.69-2A>C | splice_acceptor_variant, intron_variant | Intron 1 of 4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PET100 | ENST00000594797.6 | c.28-2A>C | splice_acceptor_variant, intron_variant | Intron 1 of 3 | 1 | NM_001171155.2 | ENSP00000470539.1 | |||
ENSG00000268400 | ENST00000698368.1 | n.28-2A>C | splice_acceptor_variant, intron_variant | Intron 1 of 19 | ENSP00000513686.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152168Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000144 AC: 2AN: 1384080Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 683064
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152168Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74354
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at