18-45952604-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_020964.3(EPG5):c.1048C>T(p.Arg350Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00051 in 1,614,108 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R350H) has been classified as Uncertain significance.
Frequency
Consequence
NM_020964.3 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 |
---|---|---|---|---|---|---|---|
EPG5 | NM_020964.3 | c.1048C>T | p.Arg350Cys | missense_variant | 3/44 | ENST00000282041.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EPG5 | ENST00000282041.11 | c.1048C>T | p.Arg350Cys | missense_variant | 3/44 | 1 | NM_020964.3 | P4 |
Frequencies
GnomAD3 genomes AF: 0.00162 AC: 247AN: 152136Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000786 AC: 196AN: 249450Hom.: 0 AF XY: 0.000864 AC XY: 117AN XY: 135340
GnomAD4 exome AF: 0.000395 AC: 577AN: 1461854Hom.: 8 Cov.: 31 AF XY: 0.000518 AC XY: 377AN XY: 727232
GnomAD4 genome AF: 0.00162 AC: 247AN: 152254Hom.: 0 Cov.: 32 AF XY: 0.00180 AC XY: 134AN XY: 74452
ClinVar
Submissions by phenotype
EPG5-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 27, 2021 | 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). - |
Vici syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at