3-122662076-G-C

Variant names:

• chr3-122662076-G-C
• rs790116
• ENST00000464704.1:n.1464G>C

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.01
• Publications: 6 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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	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.: 32

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.: 22 AF XY: 0.381 AC XY: 233313 AN XY: 612772

African (AFR) AF: 0.453 AC: 12863 AN: 28426

American (AMR) AF: 0.564 AC: 24776 AN: 43894

Ashkenazi Jewish (ASJ) AF: 0.369 AC: 8966 AN: 24278

East Asian (EAS) AF: 0.532 AC: 20389 AN: 38298

South Asian (SAS) AF: 0.415 AC: 33538 AN: 80734

European-Finnish (FIN) AF: 0.518 AC: 27081 AN: 52326

Middle Eastern (MID) AF: 0.422 AC: 2153 AN: 5098

European-Non Finnish (NFE) AF: 0.350 AC: 309236 AN: 883960

Other (OTH) AF: 0.391 AC: 20184 AN: 51560

GnomAD4 genome AF: 0.417 AC: 63354 AN: 152016 Hom.: 13449 Cov.: 32 AF XY: 0.426 AC XY: 31636 AN XY: 74312

African (AFR) AF: 0.454 AC: 18827 AN: 41452

American (AMR) AF: 0.462 AC: 7060 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.369 AC: 1280 AN: 3472

East Asian (EAS) AF: 0.514 AC: 2661 AN: 5174

South Asian (SAS) AF: 0.407 AC: 1964 AN: 4820

European-Finnish (FIN) AF: 0.529 AC: 5581 AN: 10542

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.364 AC: 24747 AN: 67956

Other (OTH) AF: 0.416 AC: 879 AN: 2112

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
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs790116; hg19: chr3-122380923;