rs922734815

Variant names:

• chr15-39934242-C-G
• rs922734815
• NM_001013703.4:c.47C>G

Your query was ambiguous. Multiple possible variants found:

• chr15-39934242-C-G
• chr15-39934242-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001013703.4(EIF2AK4):​c.47C>G​(p.Pro16Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000687 in 1,455,136 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 6.9e-7 (0 hom.)
• Consequence: EIF2AK4 NM_001013703.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.14

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.09794155).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EIF2AK4	NM_001013703.4	c.47C>G	p.Pro16Arg	missense_variant	Exon 1 of 39	ENST00000263791.10	NP_001013725.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EIF2AK4	ENST00000263791.10	c.47C>G	p.Pro16Arg	missense_variant	Exon 1 of 39	2	NM_001013703.4	ENSP00000263791.5
EIF2AK4	ENST00000559624.5	c.47C>G	p.Pro16Arg	missense_variant	Exon 1 of 11	1		ENSP00000453148.1
EIF2AK4	ENST00000560648.1	c.47C>G	p.Pro16Arg	missense_variant	Exon 1 of 4	3		ENSP00000453968.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 6.87e-7 AC: 1 AN: 1455136 Hom.: 0 Cov.: 29 AF XY: 0.00000138 AC XY: 1 AN XY: 723558

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 9.01e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

Bravo AF: 0.00000756

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.082
BayesDel_addAF	Benign	-0.095	T
BayesDel_noAF	Benign	-0.37
CADD	Benign	20
DANN	Benign	0.91
DEOGEN2	Benign	0.061	.;T;T
Eigen	Benign	-0.65
Eigen_PC	Benign	-0.60
FATHMM_MKL	Benign	0.30	N
LIST_S2	Benign	0.73	T;T;T
M_CAP	Uncertain	0.093	D
MetaRNN	Benign	0.098	T;T;T
MetaSVM	Benign	-0.96	T
MutationAssessor	Benign	0.81	L;L;.
PrimateAI	Uncertain	0.71	T
PROVEAN	Benign	-0.61	N;N;N
REVEL	Benign	0.078
Sift	Benign	0.048	D;T;D
Sift4G	Uncertain	0.029	D;T;D
Polyphen		0.16	B;B;.
Vest4		0.24
MutPred		0.20		Loss of catalytic residue at P15 (P = 0.0185);Loss of catalytic residue at P15 (P = 0.0185);Loss of catalytic residue at P15 (P = 0.0185);
MVP		0.73
MPC		0.25
ClinPred		0.19	T
GERP RS		3.5
Varity_R		0.054
gMVP		0.35

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs922734815; hg19: chr15-40226443;