rs10505283

chr8-116669336-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_003756.3(EIF3H):c.290-10356G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0451 in 152,212 control chromosomes in the GnomAD database, including 265 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 0.045 (265 hom., cov: 32)
• Consequence: EIF3H NM_003756.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.537

Genes affected

EIF3H (HGNC:3273): (eukaryotic translation initiation factor 3 subunit H) Enables deubiquitinase activity. Contributes to translation initiation factor activity. Involved in negative regulation of proteasomal ubiquitin-dependent protein catabolic process and translational initiation. Located in extracellular exosome and membrane. Part of eukaryotic translation initiation factor 3 complex. Implicated in breast cancer; prostate cancer; and prostate carcinoma. Biomarker of prostate cancer. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.27).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EIF3H	NM_003756.3	c.290-10356G>A		intron_variant		ENST00000521861.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EIF3H	ENST00000521861.6	c.290-10356G>A		intron_variant		1	NM_003756.3	P1

Frequencies

GnomAD3 genomes AF: 0.0451 AC: 6857 AN: 152094 Hom.: 264 Cov.: 32

Gnomad AFR AF: 0.0111

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.0268

Gnomad EAS AF: 0.0533

Gnomad SAS AF: 0.0617

Gnomad FIN AF: 0.0255

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0446

Gnomad OTH AF: 0.0574

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

GnomAD4 genome AF: 0.0451 AC: 6868 AN: 152212 Hom.: 265 Cov.: 32 AF XY: 0.0462 AC XY: 3440 AN XY: 74428

Gnomad4 AFR AF: 0.0111

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.0268

Gnomad4 EAS AF: 0.0534

Gnomad4 SAS AF: 0.0610

Gnomad4 FIN AF: 0.0255

Gnomad4 NFE AF: 0.0446

Gnomad4 OTH AF: 0.0610

Alfa AF: 0.0438 Hom.: 22

Bravo AF: 0.0532

Asia WGS AF: 0.0650 AC: 226 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.27
Cadd	Benign	15
Dann	Benign	0.64

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs10505283; hg19: chr8-117681575;