ENST00000419025.1:n.-119T>C

Variant names:

• chr3-184027875-A-G
• rs939335
• ENST00000419025.1:n.-119T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000419025.1(EEF1A1P8):​n.-119T>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.533 in 257,786 control chromosomes in the GnomAD database, including 38,478 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 0.57 (25497 hom., cov: 30)
  • Exomes 𝑓: 0.48 (12981 hom.)
• Consequence: EEF1A1P8 ENST00000419025.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.764

Genes affected

EEF1A1P8 (HGNC:3203): (eukaryotic translation elongation factor 1 alpha 1 pseudogene 8)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.761 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EEF1A1P8	ENST00000419025.1	n.-119T>C		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.568 AC: 86081 AN: 151608 Hom.: 25458 Cov.: 30

Gnomad AFR AF: 0.729

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.780

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.568

GnomAD4 exome AF: 0.482 AC: 51097 AN: 106060 Hom.: 12981 AF XY: 0.487 AC XY: 28600 AN XY: 58780

Gnomad4 AFR exome AF: 0.691

Gnomad4 AMR exome AF: 0.487

Gnomad4 ASJ exome AF: 0.492

Gnomad4 EAS exome AF: 0.762

Gnomad4 SAS exome AF: 0.481

Gnomad4 FIN exome AF: 0.396

Gnomad4 NFE exome AF: 0.468

Gnomad4 OTH exome AF: 0.479

GnomAD4 genome AF: 0.568 AC: 86176 AN: 151726 Hom.: 25497 Cov.: 30 AF XY: 0.562 AC XY: 41685 AN XY: 74136

Gnomad4 AFR AF: 0.729

Gnomad4 AMR AF: 0.543

Gnomad4 ASJ AF: 0.508

Gnomad4 EAS AF: 0.781

Gnomad4 SAS AF: 0.518

Gnomad4 FIN AF: 0.401

Gnomad4 NFE AF: 0.493

Gnomad4 OTH AF: 0.575

Alfa AF: 0.505 Hom.: 39307

Bravo AF: 0.585

Asia WGS AF: 0.689 AC: 2397 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.9
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs939335; hg19: chr3-183745663;