2-37156172-A-G

Position:

• chr2-37156172-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001135651.3(EIF2AK2):​c.-184+736T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.456 in 151,828 control chromosomes in the GnomAD database, including 16,272 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.46 (16272 hom., cov: 30)
• Consequence: EIF2AK2 NM_001135651.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.436

Genes affected

EIF2AK2 (HGNC:9437): (eukaryotic translation initiation factor 2 alpha kinase 2) The protein encoded by this gene is a serine/threonine protein kinase that is activated by autophosphorylation after binding to dsRNA. The activated form of the encoded protein can phosphorylate translation initiation factor EIF2S1, which in turn inhibits protein synthesis. This protein is also activated by manganese ions and heparin. The encoded protein plays an important role in the innate immune response against multiple DNA and RNA viruses. [provided by RefSeq, Jul 2021]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.752 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EIF2AK2	NM_001135651.3	c.-184+736T>C		intron_variant		ENST00000233057.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EIF2AK2	ENST00000233057.9	c.-184+736T>C		intron_variant		2	NM_001135651.3	P2

Frequencies

GnomAD3 genomes AF: 0.456 AC: 69134 AN: 151710 Hom.: 16270 Cov.: 30

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.361

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.771

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.491

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.456 AC: 69166 AN: 151828 Hom.: 16272 Cov.: 30 AF XY: 0.462 AC XY: 34260 AN XY: 74206

Gnomad4 AFR AF: 0.377

Gnomad4 AMR AF: 0.426

Gnomad4 ASJ AF: 0.546

Gnomad4 EAS AF: 0.772

Gnomad4 SAS AF: 0.400

Gnomad4 FIN AF: 0.544

Gnomad4 NFE AF: 0.471

Gnomad4 OTH AF: 0.493

Alfa AF: 0.464 Hom.: 25766

Bravo AF: 0.449

Asia WGS AF: 0.548 AC: 1905 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.2
DANN	Benign	0.78

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: rs12712526; hg19: chr2-37383315;