2-37114777-T-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_ModerateBP6_Moderate
The NM_001135651.3(EIF2AK2):āc.1331A>Gā(p.Lys444Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000498 in 1,605,928 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Consequence
NM_001135651.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EIF2AK2 | NM_001135651.3 | c.1331A>G | p.Lys444Arg | missense_variant | 14/17 | ENST00000233057.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EIF2AK2 | ENST00000233057.9 | c.1331A>G | p.Lys444Arg | missense_variant | 14/17 | 2 | NM_001135651.3 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152156Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000366 AC: 9AN: 245994Hom.: 0 AF XY: 0.0000376 AC XY: 5AN XY: 133074
GnomAD4 exome AF: 0.0000461 AC: 67AN: 1453654Hom.: 0 Cov.: 30 AF XY: 0.0000470 AC XY: 34AN XY: 723098
GnomAD4 genome AF: 0.0000854 AC: 13AN: 152274Hom.: 0 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74468
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Nov 27, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at