rs6081369

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EEF1A1P34		n.18782522G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EEF1A1P34	ENST00000419888.1	n.1169C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6

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 v4.3

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;