chr11-125893967-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_031307.4(PUS3):c.1264G>A(p.Gly422Arg) variant causes a missense change. The variant allele was found at a frequency of 0.000537 in 1,614,132 control chromosomes in the GnomAD database, including 10 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. G422V) has been classified as Uncertain significance.
Frequency
Consequence
NM_031307.4 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 |
---|---|---|---|---|---|---|---|
PUS3 | NM_031307.4 | c.1264G>A | p.Gly422Arg | missense_variant | 4/4 | ENST00000227474.8 | |
HYLS1 | NM_001134793.2 | c.-26+2495C>T | intron_variant | ENST00000425380.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PUS3 | ENST00000227474.8 | c.1264G>A | p.Gly422Arg | missense_variant | 4/4 | 1 | NM_031307.4 | P1 | |
HYLS1 | ENST00000425380.7 | c.-26+2495C>T | intron_variant | 3 | NM_001134793.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000559 AC: 85AN: 152136Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00138 AC: 347AN: 251460Hom.: 3 AF XY: 0.00129 AC XY: 175AN XY: 135912
GnomAD4 exome AF: 0.000535 AC: 782AN: 1461878Hom.: 10 Cov.: 33 AF XY: 0.000513 AC XY: 373AN XY: 727240
GnomAD4 genome AF: 0.000552 AC: 84AN: 152254Hom.: 0 Cov.: 32 AF XY: 0.000564 AC XY: 42AN XY: 74442
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Oct 14, 2023 | - - |
PUS3-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 28, 2019 | This variant is classified as 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