rs144057685
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBS1_SupportingBS2
The ENST00000682892.1(EIF2AK3):c.-145-13622A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00798 in 586,120 control chromosomes in the GnomAD database, including 30 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
ENST00000682892.1 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EIF2AK3 | XM_047446428.1 | c.17+214A>G | intron_variant | Intron 1 of 16 | XP_047302384.1 | |||
EIF2AK3 | NM_004836.7 | c.-201A>G | upstream_gene_variant | ENST00000303236.9 | NP_004827.4 | |||
EIF2AK3 | XM_047446430.1 | c.-201A>G | upstream_gene_variant | XP_047302386.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EIF2AK3 | ENST00000682892.1 | c.-145-13622A>G | intron_variant | Intron 2 of 17 | ENSP00000507214.1 | |||||
EIF2AK3 | ENST00000303236.9 | c.-201A>G | upstream_gene_variant | 1 | NM_004836.7 | ENSP00000307235.3 | ||||
EIF2AK3 | ENST00000652423.1 | n.-201A>G | upstream_gene_variant | ENSP00000498948.1 |
Frequencies
GnomAD3 genomes AF: 0.00661 AC: 1006AN: 152200Hom.: 4 Cov.: 32
GnomAD4 exome AF: 0.00846 AC: 3672AN: 433802Hom.: 26 Cov.: 6 AF XY: 0.00863 AC XY: 1879AN XY: 217852
GnomAD4 genome AF: 0.00660 AC: 1005AN: 152318Hom.: 4 Cov.: 32 AF XY: 0.00596 AC XY: 444AN XY: 74488
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
EIF2AK3: BS1, BS2 -
- -
not specified Uncertain:1
- -
Wolcott-Rallison dysplasia Uncertain:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at