15-39976797-G-GGACGAC
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 1P and 16B. PP3BP6_Very_StrongBA1
The NM_001013703.4(EIF2AK4):c.2208_2213dupCGACGA(p.Asp736_Asp737dup) variant causes a disruptive inframe insertion change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.107 in 1,574,298 control chromosomes in the GnomAD database, including 10,196 homozygotes. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001013703.4 disruptive_inframe_insertion
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EIF2AK4 | ENST00000263791.10 | c.2208_2213dupCGACGA | p.Asp736_Asp737dup | disruptive_inframe_insertion | Exon 12 of 39 | 2 | NM_001013703.4 | ENSP00000263791.5 | ||
EIF2AK4 | ENST00000560855.5 | c.1623_1628dupCGACGA | p.Asp541_Asp542dup | disruptive_inframe_insertion | Exon 8 of 34 | 5 | ENSP00000453575.1 |
Frequencies
GnomAD3 genomes AF: 0.0851 AC: 12947AN: 152202Hom.: 734 Cov.: 32
GnomAD3 exomes AF: 0.0989 AC: 20279AN: 205028Hom.: 1347 AF XY: 0.107 AC XY: 12096AN XY: 113398
GnomAD4 exome AF: 0.109 AC: 155655AN: 1421982Hom.: 9462 Cov.: 31 AF XY: 0.113 AC XY: 79605AN XY: 705002
GnomAD4 genome AF: 0.0850 AC: 12945AN: 152316Hom.: 734 Cov.: 32 AF XY: 0.0885 AC XY: 6591AN XY: 74470
ClinVar
Submissions by phenotype
not specified Benign:2
Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -
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. -
not provided Benign:2
- -
- -
Familial pulmonary capillary hemangiomatosis Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at