15-39934243-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001013703.4(EIF2AK4):c.48G>A(p.Pro16Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000177 in 1,607,614 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001013703.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EIF2AK4 | ENST00000263791.10 | c.48G>A | p.Pro16Pro | synonymous_variant | Exon 1 of 39 | 2 | NM_001013703.4 | ENSP00000263791.5 | ||
EIF2AK4 | ENST00000559624.5 | c.48G>A | p.Pro16Pro | synonymous_variant | Exon 1 of 11 | 1 | ENSP00000453148.1 | |||
EIF2AK4 | ENST00000560648.1 | c.48G>A | p.Pro16Pro | synonymous_variant | Exon 1 of 4 | 3 | ENSP00000453968.1 |
Frequencies
GnomAD3 genomes AF: 0.0000855 AC: 13AN: 152072Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000520 AC: 12AN: 230678Hom.: 0 AF XY: 0.0000551 AC XY: 7AN XY: 126978
GnomAD4 exome AF: 0.000186 AC: 271AN: 1455542Hom.: 0 Cov.: 29 AF XY: 0.000174 AC XY: 126AN XY: 723834
GnomAD4 genome AF: 0.0000855 AC: 13AN: 152072Hom.: 0 Cov.: 33 AF XY: 0.0000808 AC XY: 6AN XY: 74284
ClinVar
Submissions by phenotype
not provided Benign:1
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EIF2AK4-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). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at