chr2-61017768-C-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_002618.4(PEX13):c.9C>G(p.Ser3=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000573 in 1,397,214 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 Likely benign (★). 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 -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PEX13 | NM_002618.4 | c.9C>G | p.Ser3= | synonymous_variant | 1/4 | ENST00000295030.6 | |
PUS10 | NM_144709.4 | c.-16+240G>C | intron_variant | ENST00000316752.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PEX13 | ENST00000295030.6 | c.9C>G | p.Ser3= | synonymous_variant | 1/4 | 1 | NM_002618.4 | P1 | |
PUS10 | ENST00000316752.11 | c.-16+240G>C | intron_variant | 1 | NM_144709.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 0.00000573 AC: 8AN: 1397214Hom.: 0 Cov.: 31 AF XY: 0.00000871 AC XY: 6AN XY: 689042
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Peroxisome biogenesis disorder 11A (Zellweger) Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 27, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.