ENST00000723623.1:n.573-8597T>C

Variant names:

• chr3-184125347-A-G
• rs6806377
• ENST00000723623.1:n.573-8597T>C

Variant summary

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

The ENST00000723623.1(EIF2B5-DT):​n.573-8597T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.548 in 151,966 control chromosomes in the GnomAD database, including 23,449 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 0.55 (23449 hom., cov: 32)
• Consequence: EIF2B5-DT ENST00000723623.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.875
• Publications: 10 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.678 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000723623.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EIF2B5-DT	ENST00000723623.1		n.573-8597T>C		intron	N/A
	EIF2B5-DT	ENST00000723624.1		n.826-8597T>C		intron	N/A
	EIF2B5-DT	ENST00000723625.1		n.213-8597T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.548 AC: 83272 AN: 151848 Hom.: 23430 Cov.: 32

Gnomad AFR AF: 0.684

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.556

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

GnomAD4 genome AF: 0.548 AC: 83337 AN: 151966 Hom.: 23449 Cov.: 32 AF XY: 0.545 AC XY: 40470 AN XY: 74266

African (AFR) AF: 0.684 AC: 28348 AN: 41432

American (AMR) AF: 0.507 AC: 7727 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.540 AC: 1873 AN: 3470

East Asian (EAS) AF: 0.400 AC: 2069 AN: 5168

South Asian (SAS) AF: 0.469 AC: 2264 AN: 4826

European-Finnish (FIN) AF: 0.497 AC: 5247 AN: 10548

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.500 AC: 33953 AN: 67962

Other (OTH) AF: 0.551 AC: 1161 AN: 2106

Alfa AF: 0.518 Hom.: 65049

Bravo AF: 0.558

Asia WGS AF: 0.463 AC: 1613 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.8
DANN	Benign	0.77
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs6806377; hg19: chr3-183843135;