rs61744077
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_020964.3(EPG5):āc.3493A>Gā(p.Ile1165Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0012 in 1,614,080 control chromosomes in the GnomAD database, including 17 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I1165L) 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.3493A>G | p.Ile1165Val | missense_variant | 19/44 | ENST00000282041.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EPG5 | ENST00000282041.11 | c.3493A>G | p.Ile1165Val | missense_variant | 19/44 | 1 | NM_020964.3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00615 AC: 936AN: 152116Hom.: 12 Cov.: 32
GnomAD3 exomes AF: 0.00148 AC: 370AN: 249510Hom.: 6 AF XY: 0.00103 AC XY: 140AN XY: 135360
GnomAD4 exome AF: 0.000686 AC: 1003AN: 1461846Hom.: 6 Cov.: 31 AF XY: 0.000595 AC XY: 433AN XY: 727228
GnomAD4 genome ? AF: 0.00615 AC: 936AN: 152234Hom.: 11 Cov.: 32 AF XY: 0.00606 AC XY: 451AN XY: 74462
ClinVar
Submissions by phenotype
EPG5-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 07, 2023 | 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). - |
Vici syndrome Benign:1
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