rs10937470

Positions:

• chr3-191283019-C-T

Variant summary

Our verdict is Benign. Variant got -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

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=-0.79).
• 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/exons	MANE	Protein	UniProt
UTS2B	NM_198152.5	c.-124-706G>A		intron_variant		ENST00000340524.10	NP_937795.2
UTS2B	XM_011512631.3	c.-124-706G>A		intron_variant			XP_011510933.1
UTS2B	XM_017006091.2	c.-124-706G>A		intron_variant			XP_016861580.1
UTS2B	XM_047447899.1	c.-124-706G>A		intron_variant			XP_047303855.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UTS2B	ENST00000340524.10	c.-124-706G>A		intron_variant		2	NM_198152.5	ENSP00000340526	P1
UTS2B	ENST00000432514.5	c.-124-706G>A		intron_variant		5		ENSP00000401028
UTS2B	ENST00000463450.1	n.184-706G>A		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.260

Gnomad4 AMR AF: 0.588

Gnomad4 ASJ AF: 0.658

Gnomad4 EAS AF: 0.569

Gnomad4 SAS AF: 0.532

Gnomad4 FIN AF: 0.611

Gnomad4 NFE AF: 0.608

Gnomad4 OTH AF: 0.545

Alfa AF: 0.599 Hom.: 41928

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

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: rs10937470; hg19: chr3-191000808;