chr6-42978338-C-A
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_000287.4(PEX6):c.813G>T(p.Ala271Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000919 in 1,614,172 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000287.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PEX6 | NM_000287.4 | c.813G>T | p.Ala271Ala | synonymous_variant | Exon 1 of 17 | ENST00000304611.13 | NP_000278.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PEX6 | ENST00000304611.13 | c.813G>T | p.Ala271Ala | synonymous_variant | Exon 1 of 17 | 1 | NM_000287.4 | ENSP00000303511.8 | ||
PEX6 | ENST00000244546.4 | c.813G>T | p.Ala271Ala | synonymous_variant | Exon 1 of 15 | 1 | ENSP00000244546.4 |
Frequencies
GnomAD3 genomes AF: 0.00537 AC: 817AN: 152184Hom.: 6 Cov.: 31
GnomAD3 exomes AF: 0.00141 AC: 354AN: 251460Hom.: 3 AF XY: 0.000979 AC XY: 133AN XY: 135912
GnomAD4 exome AF: 0.000456 AC: 667AN: 1461870Hom.: 3 Cov.: 31 AF XY: 0.000408 AC XY: 297AN XY: 727238
GnomAD4 genome AF: 0.00536 AC: 817AN: 152302Hom.: 6 Cov.: 31 AF XY: 0.00508 AC XY: 378AN XY: 74462
ClinVar
Submissions by phenotype
not specified Benign:3
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not provided Benign:2
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Peroxisome biogenesis disorder 4A (Zellweger) Benign:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign. -
Zellweger spectrum disorders Benign:1
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Peroxisome biogenesis disorder Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at