chr2-88583496-T-A
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_004836.7(EIF2AK3):c.1697A>T(p.Asp566Val) variant causes a missense change. The variant allele was found at a frequency of 0.00415 in 1,613,262 control chromosomes in the GnomAD database, including 20 homozygotes. In-silico tool predicts 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 Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00258 AC: 393AN: 152176Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00260 AC: 653AN: 250846Hom.: 1 AF XY: 0.00249 AC XY: 337AN XY: 135574
GnomAD4 exome AF: 0.00432 AC: 6307AN: 1460968Hom.: 20 Cov.: 31 AF XY: 0.00415 AC XY: 3015AN XY: 726836
GnomAD4 genome AF: 0.00258 AC: 393AN: 152294Hom.: 0 Cov.: 32 AF XY: 0.00208 AC XY: 155AN XY: 74492
ClinVar
Submissions by phenotype
not provided Uncertain:2Benign:2
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EIF2AK3: BP4, BS2 -
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Wolcott-Rallison dysplasia Uncertain:2Benign:1
The EIF2AK3 c.1697A>T; p.Asp566Val variant (rs55791823), to our knowledge, is not reported in the medical literature in individuals with Wolcott-Rallison syndrome. This variant is reported in ClinVar (Variation ID: 337412) and is found in the general population with an overall allele frequency of 0.26% (730/282,242 alleles, including 1 homozygote) in the Genome Aggregation Database. Computational analyses are uncertain whether this variant is neutral or deleterious (REVEL: 0.384). Due to limited information, the clinical significance of this variant is uncertain at this time. -
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. -
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not specified Uncertain:1
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Connective tissue disorder Uncertain:1
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EIF2AK3-related disorder Benign:1
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). -
Monogenic diabetes Benign:1
ACMG criteria: BA1 (0.5% in EurNF in gnomAD), BS2 (1 homozygotes in gnomAD)= benign (REVEL 0.384 + PP3/4 predictors) + BP4/5 predictors= conflicting evidence, not using) -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at