Genetic Variant EIF4BP8:n.1464G>C (chr3-122662076-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000464704.1(EIF4BP8):n.1464G>C 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 0.384 in 1,360,590 control chromosomes in the GnomAD database, including 103,648 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 0.42 ( 13449 hom., cov: 32)

Exomes 𝑓: 0.38 ( 90199 hom. )

Consequence

EIF4BP8
ENST00000464704.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.01

Variant links:

Genes affected

EIF4BP8 (HGNC:37941): (eukaryotic translation initiation factor 4B pseudogene 8)

EIF4BP8 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EIF4BP8		n.122662076G>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EIF4BP8	ENST00000464704.1 link	n.1464G>C		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes

AF:

0.417

AC:

63298

AN:

151898

Hom.:

13428

Cov.:

show subpopulations

Gnomad AFR

AF:

0.455

Gnomad AMI

AF:

0.260

Gnomad AMR

AF:

0.461

Gnomad ASJ

AF:

0.369

Gnomad EAS

AF:

0.514

Gnomad SAS

AF:

0.405

Gnomad FIN

AF:

0.529

Gnomad MID

AF:

0.383

Gnomad NFE

AF:

0.364

Gnomad OTH

AF:

0.417

GnomAD4 exome

AF:

0.380

AC:

459186

AN:

1208574

Hom.:

90199

Cov.:

AF XY:

0.381

AC XY:

233313

AN XY:

612772

show subpopulations

Gnomad4 AFR exome

AF:

0.453

Gnomad4 AMR exome

AF:

0.564

Gnomad4 ASJ exome

AF:

0.369

Gnomad4 EAS exome

AF:

0.532

Gnomad4 SAS exome

AF:

0.415

Gnomad4 FIN exome

AF:

0.518

Gnomad4 NFE exome

AF:

0.350

Gnomad4 OTH exome

AF:

0.391

GnomAD4 genome

AF:

0.417

AC:

63354

AN:

152016

Hom.:

13449

Cov.:

AF XY:

0.426

AC XY:

31636

AN XY:

74312

show subpopulations

Gnomad4 AFR

AF:

0.454

Gnomad4 AMR

AF:

0.462

Gnomad4 ASJ

AF:

0.369

Gnomad4 EAS

AF:

0.514

Gnomad4 SAS

AF:

0.407

Gnomad4 FIN

AF:

0.529

Gnomad4 NFE

AF:

0.364

Gnomad4 OTH

AF:

0.416

Alfa

AF:

0.272

Hom.:

683

Bravo

AF:

0.416

Asia WGS

AF:

0.439

AC:

1528

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

7.3

DANN

Benign

0.39

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over