8-108279004-T-C

Variant names:

• chr8-108279004-T-C
• rs1975804
• ENST00000677614.1:c.-57-10582A>G

Variant summary

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

The ENST00000677614.1(EIF3E):​c.-57-10582A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 152,166 control chromosomes in the GnomAD database, including 3,900 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 0.20 (3900 hom., cov: 32)
• Consequence: EIF3E ENST00000677614.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.751
• Publications: 12 publications found

Genes affected

EIF3E (HGNC:3277): (eukaryotic translation initiation factor 3 subunit E) Enables protein N-terminus binding activity. Contributes to translation initiation factor activity. Involved in positive regulation of mRNA binding activity; regulation of gene expression; and translational initiation. Located in cytosol and nucleus. Part of eukaryotic translation initiation factor 3 complex. Colocalizes with PML body. [provided by Alliance of Genome Resources, Apr 2022]

LOC105375704 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.445 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000677614.1. 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
	EIF3E	ENST00000677614.1		c.-57-10582A>G		intron	N/A	ENSP00000504788.1	A0A7I2V4B4
	EIF3E	ENST00000678023.1		c.-57-10582A>G		intron	N/A	ENSP00000502937.1	A0A7I2V4B4
	EIF3E	ENST00000678334.1		c.-57-10582A>G		intron	N/A	ENSP00000503856.1	A0A7I2V4B4

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31167 AN: 152046 Hom.: 3901 Cov.: 32

Gnomad AFR AF: 0.0696

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.194

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.205 AC: 31165 AN: 152166 Hom.: 3900 Cov.: 32 AF XY: 0.207 AC XY: 15377 AN XY: 74398

African (AFR) AF: 0.0695 AC: 2886 AN: 41546

American (AMR) AF: 0.293 AC: 4478 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 539 AN: 3468

East Asian (EAS) AF: 0.460 AC: 2377 AN: 5164

South Asian (SAS) AF: 0.239 AC: 1150 AN: 4818

European-Finnish (FIN) AF: 0.218 AC: 2304 AN: 10588

Middle Eastern (MID) AF: 0.195 AC: 57 AN: 292

European-Non Finnish (NFE) AF: 0.245 AC: 16655 AN: 67998

Other (OTH) AF: 0.202 AC: 427 AN: 2110

Alfa AF: 0.225 Hom.: 13284

Bravo AF: 0.204

Asia WGS AF: 0.308 AC: 1070 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.086
DANN	Benign	0.23
PhyloP100		-0.75

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1975804;

hg19: chr8-109291233;