2-61017692-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBS1_SupportingBS2
The ENST00000401576.1(PEX13):c.-64-4C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00121 in 1,295,270 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000401576.1 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PUS10 | NM_144709.4 | c.-16+316G>A | intron_variant | ENST00000316752.11 | |||
PEX13 | NM_002618.4 | upstream_gene_variant | ENST00000295030.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PUS10 | ENST00000316752.11 | c.-16+316G>A | intron_variant | 1 | NM_144709.4 | P1 | |||
PEX13 | ENST00000295030.6 | upstream_gene_variant | 1 | NM_002618.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00188 AC: 286AN: 152204Hom.: 10 Cov.: 32
GnomAD4 exome AF: 0.00113 AC: 1286AN: 1142948Hom.: 1 Cov.: 15 AF XY: 0.00108 AC XY: 613AN XY: 569748
GnomAD4 genome AF: 0.00188 AC: 286AN: 152322Hom.: 10 Cov.: 32 AF XY: 0.00181 AC XY: 135AN XY: 74476
ClinVar
Submissions by phenotype
Peroxisome biogenesis disorder 1A (Zellweger) Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at