rs790116

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr3-122662076-G-A
• chr3-122662076-G-C

Variant summary

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

The ENST00000464704.1(EIF4BP8):​n.1464G>A variant causes a non coding transcript exon 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)
  • Exomes 𝑓: 8.3e-7 (0 hom.)
  • Failed GnomAD Quality Control
• 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: 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=-0.75).

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 8.26e-7 AC: 1 AN: 1211236 Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0 AN XY: 614032

African (AFR) AF: 0.00 AC: 0 AN: 28496

American (AMR) AF: 0.0000228 AC: 1 AN: 43934

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 24330

East Asian (EAS) AF: 0.00 AC: 0 AN: 38304

South Asian (SAS) AF: 0.00 AC: 0 AN: 80822

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 52356

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5120

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 886216

Other (OTH) AF: 0.00 AC: 0 AN: 51658

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 683

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	9.3
DANN	Benign	0.86
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;