rs1427395

Positions:

• chr2-152877408-T-A
• chr2-152877408-T-C
• chr2-152877408-T-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UBQLN4P2	ENST00000446233.1	n.589T>A		non_coding_transcript_exon_variant	1/1

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

Gnomad4 AFR exome AF: 0.401

Gnomad4 AMR exome AF: 0.497

Gnomad4 ASJ exome AF: 0.766

Gnomad4 EAS exome AF: 0.415

Gnomad4 SAS exome AF: 0.628

Gnomad4 FIN exome AF: 0.664

Gnomad4 NFE exome AF: 0.617

Gnomad4 OTH exome AF: 0.600

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

Gnomad4 AFR AF: 0.305

Gnomad4 AMR AF: 0.399

Gnomad4 ASJ AF: 0.663

Gnomad4 EAS AF: 0.275

Gnomad4 SAS AF: 0.495

Gnomad4 FIN AF: 0.583

Gnomad4 NFE AF: 0.501

Gnomad4 OTH AF: 0.510

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1427395; hg19: chr2-153733922;