12-7209754-G-A
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001351132.2(PEX5):c.1632G>A(p.Ala544=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00144 in 1,571,076 control chromosomes in the GnomAD database, including 16 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. A544A) has been classified as Likely benign.
Frequency
Consequence
NM_001351132.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PEX5 | NM_001351132.2 | c.1632G>A | p.Ala544= | synonymous_variant | 15/16 | ENST00000675855.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PEX5 | ENST00000675855.1 | c.1632G>A | p.Ala544= | synonymous_variant | 15/16 | NM_001351132.2 | A1 |
Frequencies
GnomAD3 genomes AF: 0.00803 AC: 956AN: 119014Hom.: 7 Cov.: 32
GnomAD3 exomes AF: 0.00197 AC: 496AN: 251466Hom.: 3 AF XY: 0.00141 AC XY: 192AN XY: 135912
GnomAD4 exome AF: 0.000909 AC: 1320AN: 1451986Hom.: 8 Cov.: 34 AF XY: 0.000777 AC XY: 561AN XY: 722322
GnomAD4 genome AF: 0.00798 AC: 950AN: 119090Hom.: 8 Cov.: 32 AF XY: 0.00833 AC XY: 482AN XY: 57880
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Peroxisome biogenesis disorder 2B Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Peroxisome biogenesis disorder 2A (Zellweger) Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at