chr15-39943351-CT-C
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_001013703.4(EIF2AK4):c.258-12del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.098 ( 247 hom., cov: 0)
Exomes 𝑓: 0.18 ( 31 hom. )
Consequence
EIF2AK4
NM_001013703.4 intron
NM_001013703.4 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.595
Genes affected
EIF2AK4 (HGNC:19687): (eukaryotic translation initiation factor 2 alpha kinase 4) This gene encodes a member of a family of kinases that phosphorylate the alpha subunit of eukaryotic translation initiation factor-2 (EIF2), resulting in the downregulaton of protein synthesis. The encoded protein responds to amino acid deprivation by binding uncharged transfer RNAs. It may also be activated by glucose deprivation and viral infection. Mutations in this gene have been found in individuals suffering from autosomal recessive pulmonary venoocclusive-disease-2. [provided by RefSeq, Mar 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant 15-39943351-CT-C is Benign according to our data. Variant chr15-39943351-CT-C is described in ClinVar as [Benign]. Clinvar id is 1292297.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EIF2AK4 | NM_001013703.4 | c.258-12del | intron_variant | ENST00000263791.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EIF2AK4 | ENST00000263791.10 | c.258-12del | intron_variant | 2 | NM_001013703.4 | P1 | |||
EIF2AK4 | ENST00000559624.5 | c.258-12del | intron_variant | 1 | |||||
EIF2AK4 | ENST00000560648.1 | c.258-12del | intron_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0984 AC: 10469AN: 106402Hom.: 245 Cov.: 0
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GnomAD3 exomes AF: 0.122 AC: 4571AN: 37334Hom.: 11 AF XY: 0.118 AC XY: 2421AN XY: 20570
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GnomAD4 exome AF: 0.184 AC: 137883AN: 750810Hom.: 31 Cov.: 0 AF XY: 0.178 AC XY: 68267AN XY: 384490
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GnomAD4 genome AF: 0.0985 AC: 10475AN: 106388Hom.: 247 Cov.: 0 AF XY: 0.101 AC XY: 5050AN XY: 49952
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 09, 2020 | - - |
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at