chr3-184027875-A-C

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000419025.1(EEF1A1P8):​n.-119T>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000159 in 258,282 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.00023 (0 hom., cov: 30)
  • Exomes 𝑓: 0.000056 (0 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: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

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>G		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.000231 AC: 35 AN: 151694 Hom.: 0 Cov.: 30

Gnomad AFR AF: 0.000582

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000394

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000589

Gnomad OTH AF: 0.000481

GnomAD4 exome AF: 0.0000564 AC: 6 AN: 106470 Hom.: 0 AF XY: 0.0000678 AC XY: 4 AN XY: 59030

African (AFR) AF: 0.000672 AC: 1 AN: 1488

American (AMR) AF: 0.000210 AC: 1 AN: 4764

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2334

East Asian (EAS) AF: 0.00 AC: 0 AN: 3382

South Asian (SAS) AF: 0.00 AC: 0 AN: 17534

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4516

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 408

European-Non Finnish (NFE) AF: 0.0000301 AC: 2 AN: 66518

Other (OTH) AF: 0.000362 AC: 2 AN: 5526

GnomAD4 genome AF: 0.000231 AC: 35 AN: 151812 Hom.: 0 Cov.: 30 AF XY: 0.000243 AC XY: 18 AN XY: 74180

African (AFR) AF: 0.000580 AC: 24 AN: 41378

American (AMR) AF: 0.000393 AC: 6 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5172

South Asian (SAS) AF: 0.00 AC: 0 AN: 4792

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10506

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0000589 AC: 4 AN: 67940

Other (OTH) AF: 0.000476 AC: 1 AN: 2102

Alfa AF: 0.00 Hom.: 88464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.5
DANN	Benign	0.56
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;