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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000464704.1. 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
	EIF4BP8	ENST00000464704.1	TSL:6	n.1464G>C		non_coding_transcript_exon	Exon 1 of 1

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 v4.9

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

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

Other links and lift over

dbSNP: rs790116;

hg19: chr3-122380923;