rs1975804

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr8-108279004-T-A
• chr8-108279004-T-C
• chr8-108279004-T-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000677614.1(EIF3E):​c.-57-10582A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375704	XR_928528.3	n.641-10582A>T		intron_variant	Intron 2 of 2
LOC105375704	XR_928529.3	n.237-10582A>T		intron_variant	Intron 2 of 2
LOC105375704	XR_928530.4	n.232-10582A>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EIF3E	ENST00000677614.1	c.-57-10582A>T		intron_variant	Intron 2 of 14			ENSP00000504788.1
EIF3E	ENST00000678023.1	c.-57-10582A>T		intron_variant	Intron 3 of 15			ENSP00000502937.1
EIF3E	ENST00000678334.1	c.-57-10582A>T		intron_variant	Intron 3 of 15			ENSP00000503856.1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.074
DANN	Benign	0.38
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs1975804; hg19: chr8-109291233;