2-61017768-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6BP7
The NM_002618.4(PEX13):c.9C>T(p.Ser3=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000445 in 1,549,342 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. S3S) has been classified as Likely benign.
Frequency
Consequence
NM_002618.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PEX13 | NM_002618.4 | c.9C>T | p.Ser3= | synonymous_variant | 1/4 | ENST00000295030.6 | |
PUS10 | NM_144709.4 | c.-16+240G>A | intron_variant | ENST00000316752.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PEX13 | ENST00000295030.6 | c.9C>T | p.Ser3= | synonymous_variant | 1/4 | 1 | NM_002618.4 | P1 | |
PUS10 | ENST00000316752.11 | c.-16+240G>A | intron_variant | 1 | NM_144709.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000855 AC: 13AN: 152128Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000529 AC: 8AN: 151242Hom.: 0 AF XY: 0.0000371 AC XY: 3AN XY: 80834
GnomAD4 exome AF: 0.0000401 AC: 56AN: 1397214Hom.: 0 Cov.: 31 AF XY: 0.0000363 AC XY: 25AN XY: 689042
GnomAD4 genome ? AF: 0.0000855 AC: 13AN: 152128Hom.: 0 Cov.: 32 AF XY: 0.0000942 AC XY: 7AN XY: 74302
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Mar 29, 2018 | - - |
Peroxisome biogenesis disorder 11A (Zellweger) Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at