7-76510758-G-A

Variant names:

• chr7-76510758-G-A
• rs1481463633
• NM_001347684.2:c.85+21G>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001347684.2(UPK3B):​c.85+21G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000143 in 1,395,094 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: UPK3B NM_001347684.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00400
• Publications: 0 publications found

Genes affected

UPK3B (HGNC:21444): (uroplakin 3B) UPK3B is a minor component of the apical plaques of mammalian urothelium that binds and dimerizes with uroplakin-1b (UPK1B; MIM 602380), one of the major conserved urothelium membrane proteins. The other major conserved integral membrane proteins of urothelial plaques are UPK1A (MIM 611557), UPK2 (MIM 611558), and UPK3A (MIM 611559) (Deng et al., 2002 [PubMed 12446744]).[supplied by OMIM, Mar 2008]

ENSG00000297839 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.056242704).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001347684.2. 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
	UPK3B	NM_001347684.2	MANE Select	c.85+21G>A		intron	N/A	NP_001334613.1	Q9BT76-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UPK3B	ENST00000334348.8	TSL:2 MANE Select	c.85+21G>A		intron	N/A	ENSP00000334938.3	Q9BT76-3
	UPK3B	ENST00000257632.9	TSL:2	c.106G>A	p.Asp36Asn	missense	Exon 1 of 4	ENSP00000257632.5	Q9BT76-1
	UPK3B	ENST00000911147.1		c.85+21G>A		intron	N/A	ENSP00000581206.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000143 AC: 2 AN: 1395094 Hom.: 0 Cov.: 30 AF XY: 0.00000146 AC XY: 1 AN XY: 685932

African (AFR) AF: 0.00 AC: 0 AN: 31788

American (AMR) AF: 0.00 AC: 0 AN: 37064

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 22040

East Asian (EAS) AF: 0.0000514 AC: 2 AN: 38892

South Asian (SAS) AF: 0.00 AC: 0 AN: 76852

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 49990

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5448

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1075688

Other (OTH) AF: 0.00 AC: 0 AN: 57332

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.15
BayesDel_addAF	Benign	-0.36	T
BayesDel_noAF	Benign	-0.76
CADD	Benign	9.5
DANN	Uncertain	0.99
DEOGEN2	Benign	0.017	T
Eigen	Benign	-1.0
Eigen_PC	Benign	-0.99
FATHMM_MKL	Benign	0.087	N
LIST_S2	Benign	0.47	T
M_CAP	Benign	0.0089	T
MetaRNN	Benign	0.056	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.0	N
PhyloP100		0.0040
PrimateAI	Benign	0.40	T
PROVEAN	Benign	-0.47	N
REVEL	Benign	0.020
Sift	Benign	0.048	D
Sift4G	Benign	0.16	T
Polyphen		0.0010	B
Vest4		0.065
MutPred		0.26		Gain of MoRF binding (P = 0.0814)
MVP		0.040
ClinPred		0.13	T
GERP RS		3.0
PromoterAI		0.011	Neutral
Varity_R		0.036
Mutation Taster		=96/4	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1481463633; hg19: chr7-76140075;