11-34960443-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_003477.3(PDHX):c.566G>A(p.Arg189His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00118 in 1,612,678 control chromosomes in the GnomAD database, including 20 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R189C) has been classified as Uncertain significance.
Frequency
Consequence
NM_003477.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDHX | NM_003477.3 | c.566G>A | p.Arg189His | missense_variant | 5/11 | ENST00000227868.9 | |
PDHX | NM_001135024.2 | c.386G>A | p.Arg129His | missense_variant | 5/11 | ||
PDHX | XM_011520390.2 | c.386G>A | p.Arg129His | missense_variant | 5/11 | ||
PDHX | NM_001166158.2 | c.342+12837G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDHX | ENST00000227868.9 | c.566G>A | p.Arg189His | missense_variant | 5/11 | 1 | NM_003477.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00617 AC: 938AN: 151936Hom.: 13 Cov.: 32
GnomAD3 exomes AF: 0.00144 AC: 361AN: 251302Hom.: 3 AF XY: 0.00117 AC XY: 159AN XY: 135840
GnomAD4 exome AF: 0.000661 AC: 966AN: 1460626Hom.: 8 Cov.: 29 AF XY: 0.000568 AC XY: 413AN XY: 726662
GnomAD4 genome AF: 0.00618 AC: 940AN: 152052Hom.: 12 Cov.: 32 AF XY: 0.00611 AC XY: 454AN XY: 74326
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 20, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Dec 30, 2016 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 24, 2013 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at