7-76515243-T-C
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001347684.2(UPK3B):c.*39T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.998 in 1,575,898 control chromosomes in the GnomAD database, including 784,655 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 0.99 ( 74367 hom., cov: 32)
Exomes 𝑓: 1.0 ( 710288 hom. )
Consequence
UPK3B
NM_001347684.2 3_prime_UTR
NM_001347684.2 3_prime_UTR
Scores
18
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -3.40
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=1.7234967E-6).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.994 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
UPK3B | NM_001347684.2 | c.*39T>C | 3_prime_UTR_variant | 6/6 | ENST00000334348.8 | NP_001334613.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
UPK3B | ENST00000334348.8 | c.*39T>C | 3_prime_UTR_variant | 6/6 | 2 | NM_001347684.2 | ENSP00000334938.3 | |||
UPK3B | ENST00000257632.9 | c.955T>C | p.Trp319Arg | missense_variant | 4/4 | 2 | ENSP00000257632.5 | |||
UPK3B | ENST00000394849.1 | c.790T>C | p.Trp264Arg | missense_variant | 5/5 | 2 | ENSP00000378319.1 |
Frequencies
GnomAD3 genomes AF: 0.988 AC: 150341AN: 152094Hom.: 74311 Cov.: 32
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GnomAD3 exomes AF: 0.997 AC: 189214AN: 189756Hom.: 94339 AF XY: 0.998 AC XY: 101664AN XY: 101890
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GnomAD4 exome AF: 0.999 AC: 1422116AN: 1423686Hom.: 710288 Cov.: 80 AF XY: 0.999 AC XY: 703865AN XY: 704522
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GnomAD4 genome AF: 0.988 AC: 150456AN: 152212Hom.: 74367 Cov.: 32 AF XY: 0.989 AC XY: 73570AN XY: 74422
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ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;.
PrimateAI
Benign
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;T
Sift4G
Benign
T;T
Polyphen
B;B
Vest4
MutPred
Gain of solvent accessibility (P = 6e-04);.;
ClinPred
T
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at