3-184149055-T-C

Variant names:

• chr3-184149055-T-C
• rs4575925
• ENST00000723789.1:n.446A>G

Variant summary

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

The ENST00000723789.1(ENSG00000294465):​n.446A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 151,814 control chromosomes in the GnomAD database, including 9,676 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 (9676 hom., cov: 31)
• Consequence: ENSG00000294465 ENST00000723789.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56
• Publications: 5 publications found

Genes affected

ENSG00000294465 (HGNC:):

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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.548 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000723789.1. 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
	ENSG00000294465	ENST00000723789.1		n.446A>G		non_coding_transcript_exon	Exon 2 of 2
	EIF2B5-DT	ENST00000723636.1		n.60+5569A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.351 AC: 53309 AN: 151696 Hom.: 9658 Cov.: 31

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.565

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.351 AC: 53358 AN: 151814 Hom.: 9676 Cov.: 31 AF XY: 0.353 AC XY: 26204 AN XY: 74166

African (AFR) AF: 0.392 AC: 16210 AN: 41376

American (AMR) AF: 0.279 AC: 4247 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.295 AC: 1024 AN: 3466

East Asian (EAS) AF: 0.565 AC: 2917 AN: 5160

South Asian (SAS) AF: 0.415 AC: 1996 AN: 4812

European-Finnish (FIN) AF: 0.312 AC: 3283 AN: 10510

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.332 AC: 22540 AN: 67936

Other (OTH) AF: 0.342 AC: 719 AN: 2104

Alfa AF: 0.288 Hom.: 2024

Bravo AF: 0.349

Asia WGS AF: 0.483 AC: 1679 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.41
DANN	Benign	0.34
PhyloP100		-1.6
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: rs4575925; hg19: chr3-183866843;