3-191328956-C-T

Position:

• chr3-191328956-C-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_198152.5(UTS2B):​c.-664-247G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0602 in 152,262 control chromosomes in the GnomAD database, including 431 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.060 (429 hom., cov: 32)
  • Exomes 𝑓: 0.11 (2 hom.)
• Consequence: UTS2B NM_198152.5 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.769

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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BP6: Variant 3-191328956-C-T is Benign according to our data. Variant chr3-191328956-C-T is described in ClinVar as [Benign]. Clinvar id is 1268024.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UTS2B	NM_198152.5	c.-664-247G>A		intron_variant		ENST00000340524.10	NP_937795.2
UTS2B	XM_011512631.3	c.-413G>A		5_prime_UTR_variant	1/8		XP_011510933.1
UTS2B	XM_017006091.2	c.-413G>A		5_prime_UTR_variant	1/8		XP_016861580.1
UTS2B	XM_047447899.1	c.-260-247G>A		intron_variant			XP_047303855.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UTS2B	ENST00000340524.10	c.-664-247G>A		intron_variant		2	NM_198152.5	ENSP00000340526	P1
UTS2B	ENST00000432514.5	c.-831-247G>A		intron_variant		5		ENSP00000401028
UTS2B	ENST00000464814.1	n.357G>A		non_coding_transcript_exon_variant	1/2	5
UTS2B	ENST00000490825.1	n.256G>A		non_coding_transcript_exon_variant	2/4	5

Frequencies

GnomAD3 genomes AF: 0.0602 AC: 9157 AN: 152090 Hom.: 429 Cov.: 32

Gnomad AFR AF: 0.0110

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0658

Gnomad ASJ AF: 0.0882

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0576

Gnomad OTH AF: 0.0489

GnomAD4 exome AF: 0.111 AC: 6 AN: 54 Hom.: 2 Cov.: 0 AF XY: 0.0833 AC XY: 3 AN XY: 36

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.111

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0602 AC: 9165 AN: 152208 Hom.: 429 Cov.: 32 AF XY: 0.0674 AC XY: 5019 AN XY: 74414

Gnomad4 AFR AF: 0.0109

Gnomad4 AMR AF: 0.0658

Gnomad4 ASJ AF: 0.0882

Gnomad4 EAS AF: 0.192

Gnomad4 SAS AF: 0.187

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.0576

Gnomad4 OTH AF: 0.0503

Alfa AF: 0.0605 Hom.: 42

Bravo AF: 0.0524

Asia WGS AF: 0.157 AC: 544 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Apr 10, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	7.2
DANN	Benign	0.67

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: rs62617841; hg19: chr3-191046745;