2-152877408-T-A

Variant names:

• chr2-152877408-T-A
• rs1427395
• ENST00000446233.1:n.589T>A

Variant summary

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

The ENST00000446233.1(UBQLN4P2):​n.589T>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 0.461 in 175,586 control chromosomes in the GnomAD database, including 19,926 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 0.44 (15702 hom., cov: 31)
  • Exomes 𝑓: 0.60 (4224 hom.)
• Consequence: UBQLN4P2 ENST00000446233.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.23
• Publications: 2 publications found

Genes affected

UBQLN4P2 (HGNC:38662): (ubiquilin 4 pseudogene 2)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.496 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000446233.1. 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
	UBQLN4P2	ENST00000446233.1	TSL:6	n.589T>A		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.440 AC: 66735 AN: 151752 Hom.: 15687 Cov.: 31

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.663

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.583

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.510

GnomAD4 exome AF: 0.599 AC: 14199 AN: 23718 Hom.: 4224 Cov.: 0 AF XY: 0.606 AC XY: 8175 AN XY: 13494

African (AFR) AF: 0.401 AC: 228 AN: 568

American (AMR) AF: 0.497 AC: 1067 AN: 2148

Ashkenazi Jewish (ASJ) AF: 0.766 AC: 302 AN: 394

East Asian (EAS) AF: 0.415 AC: 390 AN: 940

South Asian (SAS) AF: 0.628 AC: 1347 AN: 2144

European-Finnish (FIN) AF: 0.664 AC: 918 AN: 1382

Middle Eastern (MID) AF: 0.750 AC: 48 AN: 64

European-Non Finnish (NFE) AF: 0.617 AC: 9167 AN: 14858

Other (OTH) AF: 0.600 AC: 732 AN: 1220

GnomAD4 genome AF: 0.440 AC: 66791 AN: 151868 Hom.: 15702 Cov.: 31 AF XY: 0.443 AC XY: 32901 AN XY: 74210

African (AFR) AF: 0.305 AC: 12643 AN: 41418

American (AMR) AF: 0.399 AC: 6093 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.663 AC: 2300 AN: 3468

East Asian (EAS) AF: 0.275 AC: 1417 AN: 5144

South Asian (SAS) AF: 0.495 AC: 2378 AN: 4804

European-Finnish (FIN) AF: 0.583 AC: 6139 AN: 10532

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.501 AC: 34027 AN: 67936

Other (OTH) AF: 0.510 AC: 1075 AN: 2106

Alfa AF: 0.327 Hom.: 893

Bravo AF: 0.419

Asia WGS AF: 0.437 AC: 1522 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	2.9
DANN	Benign	0.60
PhyloP100		2.2

Splicing

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

Other links and lift over

dbSNP: rs1427395; hg19: chr2-153733922;