10-92669710-C-T

Variant names:

• chr10-92669710-C-T
• rs7918084
• ENST00000428356.1:n.34G>A

Variant summary

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

The ENST00000428356.1(EIF2S2P3):​n.34G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.603 in 151,516 control chromosomes in the GnomAD database, including 28,135 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 0.60 (28135 hom., cov: 29)
  • Exomes 𝑓: 0.62 (195585 hom.)
  • Failed GnomAD Quality Control
• Consequence: EIF2S2P3 ENST00000428356.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.06
• Publications: 18 publications found

Genes affected

EIF2S2P3 (HGNC:31664): (eukaryotic translation initiation factor 2 subunit 2 beta pseudogene 3)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.854 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000428356.1. 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
	EIF2S2P3	ENST00000428356.1	TSL:6	n.34G>A		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.603 AC: 91289 AN: 151398 Hom.: 28099 Cov.: 29

Gnomad AFR AF: 0.659

Gnomad AMI AF: 0.733

Gnomad AMR AF: 0.608

Gnomad ASJ AF: 0.626

Gnomad EAS AF: 0.875

Gnomad SAS AF: 0.682

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.577

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.621 AC: 625991 AN: 1008474 Hom.: 195585 Cov.: 16 AF XY: 0.619 AC XY: 317862 AN XY: 513112

African (AFR) AF: 0.682 AC: 15998 AN: 23448

American (AMR) AF: 0.697 AC: 21587 AN: 30964

Ashkenazi Jewish (ASJ) AF: 0.624 AC: 13491 AN: 21620

East Asian (EAS) AF: 0.896 AC: 32117 AN: 35852

South Asian (SAS) AF: 0.681 AC: 47915 AN: 70342

European-Finnish (FIN) AF: 0.559 AC: 25549 AN: 45740

Middle Eastern (MID) AF: 0.593 AC: 1902 AN: 3208

European-Non Finnish (NFE) AF: 0.600 AC: 439404 AN: 732668

Other (OTH) AF: 0.628 AC: 28028 AN: 44632

GnomAD4 genome AF: 0.603 AC: 91386 AN: 151516 Hom.: 28135 Cov.: 29 AF XY: 0.603 AC XY: 44638 AN XY: 74020

African (AFR) AF: 0.659 AC: 27248 AN: 41324

American (AMR) AF: 0.608 AC: 9265 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.626 AC: 2172 AN: 3468

East Asian (EAS) AF: 0.875 AC: 4495 AN: 5136

South Asian (SAS) AF: 0.682 AC: 3283 AN: 4812

European-Finnish (FIN) AF: 0.536 AC: 5563 AN: 10386

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.550 AC: 37334 AN: 67852

Other (OTH) AF: 0.578 AC: 1213 AN: 2100

Alfa AF: 0.582 Hom.: 3237

Bravo AF: 0.612

Asia WGS AF: 0.733 AC: 2547 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	1.9
DANN	Benign	0.86
PhyloP100		3.1

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7918084;

hg19: chr10-94429467;