chr3-191267258-A-G

Position:

• chr3-191267258-A-G

Variant summary

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

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
• 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]

ACMG classification

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: 37341 AN: 152094 Hom.: 5239 Cov.: 33

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.0602

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.278

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.245 AC: 37356 AN: 152210 Hom.: 5243 Cov.: 33 AF XY: 0.241 AC XY: 17955 AN XY: 74402

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.222

Gnomad4 ASJ AF: 0.317

Gnomad4 EAS AF: 0.0603

Gnomad4 SAS AF: 0.221

Gnomad4 FIN AF: 0.281

Gnomad4 NFE AF: 0.324

Gnomad4 OTH AF: 0.279

Alfa AF: 0.271 Hom.: 1192

Bravo AF: 0.236

Asia WGS AF: 0.134 AC: 468 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	11
DANN	Benign	0.88

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

Publications

LitVar

Other links and lift over

dbSNP: rs1129586; hg19: chr3-190985047;