15-39934255-G-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 2P and 11B. PM2BP4_ModerateBP6_Very_StrongBP7
The NM_001013703.4(EIF2AK4):c.60G>A(p.Pro20Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000184 in 1,610,190 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 Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EIF2AK4 | ENST00000263791.10 | c.60G>A | p.Pro20Pro | synonymous_variant | Exon 1 of 39 | 2 | NM_001013703.4 | ENSP00000263791.5 | ||
EIF2AK4 | ENST00000559624.5 | c.60G>A | p.Pro20Pro | synonymous_variant | Exon 1 of 11 | 1 | ENSP00000453148.1 | |||
EIF2AK4 | ENST00000560648.1 | c.60G>A | p.Pro20Pro | synonymous_variant | Exon 1 of 4 | 3 | ENSP00000453968.1 |
Frequencies
GnomAD3 genomes AF: 0.000118 AC: 18AN: 152138Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000550 AC: 13AN: 236434Hom.: 0 AF XY: 0.0000540 AC XY: 7AN XY: 129734
GnomAD4 exome AF: 0.000191 AC: 278AN: 1458052Hom.: 0 Cov.: 29 AF XY: 0.000153 AC XY: 111AN XY: 725216
GnomAD4 genome AF: 0.000118 AC: 18AN: 152138Hom.: 0 Cov.: 33 AF XY: 0.000135 AC XY: 10AN XY: 74330
ClinVar
Submissions by phenotype
not provided Benign:2
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
The c.60G>A variant has not been reported in the medical literature, gene specific variation databases, nor has it been previously identified by our laboratory. It is present in the genome Aggregation Database with an overall population frequency of 0.006% (15 out of 264,584 chromosomes). The guanine in exon 20 is not highly conserved, and the variant is not predicted to alter EIF2AK4 mRNA splicing (Alamut software v.2.10.0). Therefore, the c.60G>A variant is likely to be benign. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at