rs150314450
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBS1_Supporting
The NM_004836.7(EIF2AK3):c.1751G>A(p.Gly584Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000127 in 1,611,116 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_004836.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EIF2AK3 | NM_004836.7 | c.1751G>A | p.Gly584Glu | missense_variant | 10/17 | ENST00000303236.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EIF2AK3 | ENST00000303236.9 | c.1751G>A | p.Gly584Glu | missense_variant | 10/17 | 1 | NM_004836.7 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000704 AC: 107AN: 151896Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000167 AC: 42AN: 250804Hom.: 0 AF XY: 0.000133 AC XY: 18AN XY: 135574
GnomAD4 exome AF: 0.0000658 AC: 96AN: 1459106Hom.: 0 Cov.: 30 AF XY: 0.0000496 AC XY: 36AN XY: 726050
GnomAD4 genome ? AF: 0.000717 AC: 109AN: 152010Hom.: 0 Cov.: 32 AF XY: 0.000808 AC XY: 60AN XY: 74300
ClinVar
Submissions by phenotype
Wolcott-Rallison dysplasia Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 31, 2018 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | New York Genome Center | Oct 26, 2021 | - - |
Monogenic diabetes Uncertain:1
Uncertain significance, criteria provided, single submitter | research | Personalized Diabetes Medicine Program, University of Maryland School of Medicine | Oct 27, 2015 | ACMG Criteria: PP3, BS2 (type2diabetesgenetics.org), BP4 - |
Connective tissue disorder Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | Jun 22, 2021 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 13, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at