3-191267258-A-G
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_198152.5(UTS2B):c.*1158T>C variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.245 in 152,210 control chromosomes in the GnomAD database, including 5,243 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 0.25 ( 5243 hom., cov: 33)
Failed GnomAD Quality Control
Consequence
UTS2B
NM_198152.5 3_prime_UTR
NM_198152.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 4.21
Genes affected
UTS2B (HGNC:30894): (urotensin 2B) Predicted to enable G protein-coupled receptor binding activity. Predicted to be involved in regulation of blood pressure. Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]
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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 (BayesDel_noAF=-0.7).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.32 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UTS2B | NM_198152.5 | c.*1158T>C | 3_prime_UTR_variant | 9/9 | ENST00000340524.10 | ||
UTS2B | XM_011512631.3 | c.*1158T>C | 3_prime_UTR_variant | 8/8 | |||
UTS2B | XM_047447899.1 | c.*1158T>C | 3_prime_UTR_variant | 8/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UTS2B | ENST00000340524.10 | c.*1158T>C | 3_prime_UTR_variant | 9/9 | 2 | NM_198152.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.246 AC: 37341AN: 152094Hom.: 5239 Cov.: 33
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GnomAD4 exome Data not reliable, filtered out with message: AC0AC: 0AN: 0Hom.: 0 Cov.: 0AC XY: 0AN XY: 0
GnomAD4 exome
Data not reliable, filtered out with message: AC0
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GnomAD4 genome AF: 0.245 AC: 37356AN: 152210Hom.: 5243 Cov.: 33 AF XY: 0.241 AC XY: 17955AN XY: 74402
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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