rs4912474

Variant names:

• chr3-184148698-C-A
• rs4912474
• ENST00000723636.1:n.60+5926G>T

Your query was ambiguous. Multiple possible variants found:

• chr3-184148698-C-A
• chr3-184148698-C-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+5926G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 152,044 control chromosomes in the GnomAD database, including 9,484 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 0.35 (9484 hom., cov: 32)
• Consequence: EIF2B5-DT ENST00000723636.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.83
• Publications: 8 publications found

Genes affected

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

ENSG00000294465 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.525 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EIF2B5-DT	ENST00000723636.1	n.60+5926G>T		intron_variant	Intron 1 of 2
ENSG00000294465	ENST00000723789.1	n.*199G>T		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52827 AN: 151926 Hom.: 9468 Cov.: 32

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.542

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.312

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.348 AC: 52872 AN: 152044 Hom.: 9484 Cov.: 32 AF XY: 0.349 AC XY: 25968 AN XY: 74312

African (AFR) AF: 0.383 AC: 15903 AN: 41472

American (AMR) AF: 0.278 AC: 4246 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.296 AC: 1025 AN: 3468

East Asian (EAS) AF: 0.542 AC: 2797 AN: 5164

South Asian (SAS) AF: 0.412 AC: 1983 AN: 4816

European-Finnish (FIN) AF: 0.310 AC: 3274 AN: 10554

Middle Eastern (MID) AF: 0.325 AC: 95 AN: 292

European-Non Finnish (NFE) AF: 0.331 AC: 22510 AN: 67970

Other (OTH) AF: 0.337 AC: 712 AN: 2112

Alfa AF: 0.336 Hom.: 27593

Bravo AF: 0.345

Asia WGS AF: 0.476 AC: 1654 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.24
DANN	Benign	0.35
PhyloP100		-1.8
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: rs4912474; hg19: chr3-183866486;