3-184027875-A-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 27 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000419025.1. 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
	EEF1A1P8	ENST00000419025.1	TSL:6	n.-119T>C		upstream_gene	N/A

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

African (AFR) AF: 0.691 AC: 1027 AN: 1486

American (AMR) AF: 0.487 AC: 2313 AN: 4748

Ashkenazi Jewish (ASJ) AF: 0.492 AC: 1142 AN: 2322

East Asian (EAS) AF: 0.762 AC: 2566 AN: 3368

South Asian (SAS) AF: 0.481 AC: 8406 AN: 17474

European-Finnish (FIN) AF: 0.396 AC: 1774 AN: 4484

Middle Eastern (MID) AF: 0.569 AC: 231 AN: 406

European-Non Finnish (NFE) AF: 0.468 AC: 30996 AN: 66258

Other (OTH) AF: 0.479 AC: 2642 AN: 5514

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

African (AFR) AF: 0.729 AC: 30163 AN: 41356

American (AMR) AF: 0.543 AC: 8272 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.508 AC: 1764 AN: 3470

East Asian (EAS) AF: 0.781 AC: 4039 AN: 5170

South Asian (SAS) AF: 0.518 AC: 2478 AN: 4788

European-Finnish (FIN) AF: 0.401 AC: 4202 AN: 10488

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.493 AC: 33472 AN: 67920

Other (OTH) AF: 0.575 AC: 1208 AN: 2102

Alfa AF: 0.518 Hom.: 88464

Bravo AF: 0.585

Asia WGS AF: 0.689 AC: 2397 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.9
DANN	Benign	0.51
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs939335; hg19: chr3-183745663;