6-136822796-G-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PVS1_StrongPM2
The NM_000288.4(PEX7):c.130+1G>T variant causes a splice donor, intron change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000861 in 1,162,078 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_000288.4 splice_donor, 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 |
---|---|---|---|---|---|---|---|---|
PEX7 | NM_000288.4 | c.130+1G>T | splice_donor_variant, intron_variant | Intron 1 of 9 | ENST00000318471.5 | NP_000279.1 | ||
PEX7 | XM_006715502.3 | c.130+1G>T | splice_donor_variant, intron_variant | Intron 1 of 6 | XP_006715565.1 | |||
PEX7 | XM_047418874.1 | c.130+1G>T | splice_donor_variant, intron_variant | Intron 1 of 5 | XP_047274830.1 | |||
PEX7 | NM_001410945.1 | c.-568G>T | upstream_gene_variant | NP_001397874.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 34
GnomAD4 exome AF: 8.61e-7 AC: 1AN: 1162078Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 561660
GnomAD4 genome Cov.: 34
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at