rs1413838301
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PVS1_StrongPM2PP3_Strong
The NM_000288.4(PEX7):c.904-1G>A variant causes a splice acceptor change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000686 in 1,457,178 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. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_000288.4 splice_acceptor
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.904-1G>A | splice_acceptor_variant | ENST00000318471.5 | |||
PEX7 | NM_001410945.1 | c.790-1G>A | splice_acceptor_variant | ||||
PEX7 | XM_006715502.3 | c.610-1G>A | splice_acceptor_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PEX7 | ENST00000318471.5 | c.904-1G>A | splice_acceptor_variant | 1 | NM_000288.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251144Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135758
GnomAD4 exome AF: 6.86e-7 AC: 1AN: 1457178Hom.: 0 Cov.: 28 AF XY: 0.00 AC XY: 0AN XY: 725252
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Rhizomelic chondrodysplasia punctata type 1 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Counsyl | Sep 07, 2017 | - - |
Phytanic acid storage disease;C1859133:Rhizomelic chondrodysplasia punctata type 1;C2749346:Peroxisome biogenesis disorder 9B Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 11, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at