rs602716

Positions:

• chr11-118930526-G-A
• chr11-118930526-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000534788.1(UPK2):​n.128+5235G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.317 in 152,074 control chromosomes in the GnomAD database, including 8,614 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 0.32 (8614 hom., cov: 32)
• Consequence: UPK2 ENST00000534788.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.104

Genes affected

UPK2 (HGNC:12579): (uroplakin 2) This gene encodes one of the proteins of the highly conserved urothelium-specific integral membrane proteins of the asymmetric unit membrane which forms urothelium apical plaques in mammals. The asymmetric unit membrane is believed to strengthen the urothelium by preventing cell rupture during bladder distention. The encoded protein is expressed in the peripheral blood of bladder cancer patients with transitional cell carcinomas.[provided by RefSeq, Sep 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.435 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
UPK2	ENST00000534788.1	n.128+5235G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.317 AC: 48135 AN: 151956 Hom.: 8604 Cov.: 32

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.377

Gnomad OTH AF: 0.293

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.317 AC: 48170 AN: 152074 Hom.: 8614 Cov.: 32 AF XY: 0.319 AC XY: 23689 AN XY: 74330

Gnomad4 AFR AF: 0.164

Gnomad4 AMR AF: 0.444

Gnomad4 ASJ AF: 0.291

Gnomad4 EAS AF: 0.145

Gnomad4 SAS AF: 0.310

Gnomad4 FIN AF: 0.430

Gnomad4 NFE AF: 0.377

Gnomad4 OTH AF: 0.294

Alfa AF: 0.361 Hom.: 13595

Bravo AF: 0.311

Asia WGS AF: 0.240 AC: 835 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.1
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs602716; hg19: chr11-118801235;