chr3-184148012-T-A

Variant names:

• chr3-184148012-T-A
• rs843360
• ENST00000723636.1:n.60+6612A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000723636.1(EIF2B5-DT):​n.60+6612A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.467 in 151,820 control chromosomes in the GnomAD database, including 16,788 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 0.47 (16788 hom., cov: 31)
• Consequence: EIF2B5-DT ENST00000723636.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.580
• Publications: 2 publications found

Genes affected

EIF2B5-DT (HGNC:55202): (EIF2B5 divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.558 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000723636.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EIF2B5-DT	ENST00000723636.1		n.60+6612A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.467 AC: 70864 AN: 151702 Hom.: 16770 Cov.: 31

Gnomad AFR AF: 0.417

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.545

Gnomad SAS AF: 0.577

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.495

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.467 AC: 70921 AN: 151820 Hom.: 16788 Cov.: 31 AF XY: 0.468 AC XY: 34733 AN XY: 74174

African (AFR) AF: 0.416 AC: 17231 AN: 41380

American (AMR) AF: 0.460 AC: 7013 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 1394 AN: 3466

East Asian (EAS) AF: 0.545 AC: 2807 AN: 5152

South Asian (SAS) AF: 0.576 AC: 2774 AN: 4814

European-Finnish (FIN) AF: 0.428 AC: 4494 AN: 10498

Middle Eastern (MID) AF: 0.442 AC: 129 AN: 292

European-Non Finnish (NFE) AF: 0.495 AC: 33649 AN: 67958

Other (OTH) AF: 0.455 AC: 959 AN: 2110

Alfa AF: 0.280 Hom.: 620

Bravo AF: 0.462

Asia WGS AF: 0.564 AC: 1960 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.6
DANN	Benign	0.72
PhyloP100		0.58
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs843360; hg19: chr3-183865800;