20-18782522-G-A

Variant names:

• chr20-18782522-G-A
• rs6081369
• ENST00000419888.1:n.1169C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000419888.1(EEF1A1P34):​n.1169C>T variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.209 in 233,042 control chromosomes in the GnomAD database, including 5,277 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 0.20 (3068 hom., cov: 32)
  • Exomes 𝑓: 0.23 (2209 hom.)
• Consequence: EEF1A1P34 ENST00000419888.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.53
• Publications: 4 publications found

Genes affected

EEF1A1P34 (HGNC:37912): (eukaryotic translation elongation factor 1 alpha 1 pseudogene 34)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000419888.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EEF1A1P34	ENST00000419888.1	TSL:6	n.1169C>T		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29878 AN: 151986 Hom.: 3071 Cov.: 32

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.0957

Gnomad EAS AF: 0.0644

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.161

GnomAD4 exome AF: 0.232 AC: 18810 AN: 80938 Hom.: 2209 Cov.: 0 AF XY: 0.234 AC XY: 11386 AN XY: 48602

African (AFR) AF: 0.219 AC: 254 AN: 1158

American (AMR) AF: 0.141 AC: 317 AN: 2254

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 147 AN: 1458

East Asian (EAS) AF: 0.0509 AC: 102 AN: 2004

South Asian (SAS) AF: 0.292 AC: 3564 AN: 12206

European-Finnish (FIN) AF: 0.271 AC: 1138 AN: 4204

Middle Eastern (MID) AF: 0.159 AC: 52 AN: 328

European-Non Finnish (NFE) AF: 0.232 AC: 12271 AN: 52918

Other (OTH) AF: 0.219 AC: 965 AN: 4408

GnomAD4 genome AF: 0.196 AC: 29874 AN: 152104 Hom.: 3068 Cov.: 32 AF XY: 0.199 AC XY: 14795 AN XY: 74358

African (AFR) AF: 0.200 AC: 8274 AN: 41458

American (AMR) AF: 0.148 AC: 2265 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0957 AC: 332 AN: 3470

East Asian (EAS) AF: 0.0636 AC: 330 AN: 5188

South Asian (SAS) AF: 0.281 AC: 1357 AN: 4826

European-Finnish (FIN) AF: 0.260 AC: 2754 AN: 10574

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.206 AC: 13989 AN: 67984

Other (OTH) AF: 0.161 AC: 339 AN: 2110

Alfa AF: 0.204 Hom.: 2607

Bravo AF: 0.184

Asia WGS AF: 0.148 AC: 514 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	3.0
DANN	Benign	0.66
PhyloP100		5.5

Splicing

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

Other links and lift over

dbSNP: rs6081369; hg19: chr20-18763166;