18-45876331-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The ENST00000282041.11(EPG5):c.5954G>A(p.Arg1985Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00365 in 1,613,746 control chromosomes in the GnomAD database, including 67 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict 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. R1985W) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000282041.11 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EPG5 | NM_020964.3 | c.5954G>A | p.Arg1985Gln | missense_variant | 35/44 | ENST00000282041.11 | NP_066015.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EPG5 | ENST00000282041.11 | c.5954G>A | p.Arg1985Gln | missense_variant | 35/44 | 1 | NM_020964.3 | ENSP00000282041 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0123 AC: 1872AN: 152116Hom.: 32 Cov.: 32
GnomAD3 exomes AF: 0.00501 AC: 1251AN: 249564Hom.: 20 AF XY: 0.00428 AC XY: 579AN XY: 135396
GnomAD4 exome AF: 0.00274 AC: 4003AN: 1461512Hom.: 34 Cov.: 30 AF XY: 0.00265 AC XY: 1924AN XY: 727076
GnomAD4 genome AF: 0.0124 AC: 1882AN: 152234Hom.: 33 Cov.: 32 AF XY: 0.0120 AC XY: 892AN XY: 74422
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 11, 2020 | - - |
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Vici syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at