3-191283019-C-T

Variant names:

• chr3-191283019-C-T
• rs10937470
• NM_198152.5:c.-124-706G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_198152.5(UTS2B):​c.-124-706G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.507 in 151,558 control chromosomes in the GnomAD database, including 21,174 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 0.51 (21174 hom., cov: 32)
• Consequence: UTS2B NM_198152.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.239
• Publications: 15 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.604 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UTS2B	NM_198152.5	c.-124-706G>A		intron_variant	Intron 4 of 8	ENST00000340524.10	NP_937795.2
UTS2B	XM_017006091.2	c.-124-706G>A		intron_variant	Intron 3 of 7		XP_016861580.1
UTS2B	XM_011512631.3	c.-124-706G>A		intron_variant	Intron 3 of 7		XP_011510933.1
UTS2B	XM_047447899.1	c.-124-706G>A		intron_variant	Intron 3 of 7		XP_047303855.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UTS2B	ENST00000340524.10	c.-124-706G>A		intron_variant	Intron 4 of 8	2	NM_198152.5	ENSP00000340526.5
UTS2B	ENST00000432514.5	c.-124-706G>A		intron_variant	Intron 5 of 6	5		ENSP00000401028.1
UTS2B	ENST00000463450.1	n.184-706G>A		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.507 AC: 76788 AN: 151438 Hom.: 21159 Cov.: 32

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.440

Gnomad AMR AF: 0.587

Gnomad ASJ AF: 0.658

Gnomad EAS AF: 0.569

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.621

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.507 AC: 76835 AN: 151558 Hom.: 21174 Cov.: 32 AF XY: 0.510 AC XY: 37763 AN XY: 74028

African (AFR) AF: 0.260 AC: 10786 AN: 41408

American (AMR) AF: 0.588 AC: 8970 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.658 AC: 2284 AN: 3470

East Asian (EAS) AF: 0.569 AC: 2891 AN: 5080

South Asian (SAS) AF: 0.532 AC: 2559 AN: 4808

European-Finnish (FIN) AF: 0.611 AC: 6316 AN: 10344

Middle Eastern (MID) AF: 0.630 AC: 184 AN: 292

European-Non Finnish (NFE) AF: 0.608 AC: 41298 AN: 67876

Other (OTH) AF: 0.545 AC: 1146 AN: 2104

Alfa AF: 0.574 Hom.: 60780

Bravo AF: 0.495

Asia WGS AF: 0.547 AC: 1897 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.7
DANN	Benign	0.54
PhyloP100		0.24
Mutation Taster		=100/0	polymorphism (auto)

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: rs10937470; hg19: chr3-191000808;