6-136869951-G-A
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_StrongBP6BS1
The NM_000288.4(PEX7):c.695G>A(p.Arg232Gln) variant causes a missense change. The variant allele was found at a frequency of 0.000159 in 1,614,020 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000288.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PEX7 | NM_000288.4 | c.695G>A | p.Arg232Gln | missense_variant | Exon 7 of 10 | ENST00000318471.5 | NP_000279.1 | |
PEX7 | NM_001410945.1 | c.581G>A | p.Arg194Gln | missense_variant | Exon 7 of 10 | NP_001397874.1 | ||
PEX7 | XM_006715502.3 | c.401G>A | p.Arg134Gln | missense_variant | Exon 4 of 7 | XP_006715565.1 | ||
PEX7 | XM_047418874.1 | c.526+23770G>A | intron_variant | Intron 5 of 5 | XP_047274830.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000204 AC: 31AN: 152156Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000255 AC: 64AN: 251446Hom.: 0 AF XY: 0.000235 AC XY: 32AN XY: 135900
GnomAD4 exome AF: 0.000154 AC: 225AN: 1461746Hom.: 0 Cov.: 30 AF XY: 0.000158 AC XY: 115AN XY: 727168
GnomAD4 genome AF: 0.000204 AC: 31AN: 152274Hom.: 0 Cov.: 32 AF XY: 0.000255 AC XY: 19AN XY: 74466
ClinVar
Submissions by phenotype
Rhizomelic chondrodysplasia punctata type 1 Benign:2
- -
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). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
Peroxisome biogenesis disorder 9B Benign:2
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). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. -
- -
not provided Uncertain:1
- -
Phytanic acid storage disease;C1859133:Rhizomelic chondrodysplasia punctata type 1;C2749346:Peroxisome biogenesis disorder 9B Uncertain:1
- -
PEX7-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at