3-191328981-G-A

Position:

• chr3-191328981-G-A

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.-664-272C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 152,162 control chromosomes in the GnomAD database, including 2,890 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.17 (2888 hom., cov: 32)
  • Exomes 𝑓: 0.22 (2 hom.)
• Consequence: UTS2B NM_198152.5 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -2.47

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=-0.82).
• BP6: Variant 3-191328981-G-A is Benign according to our data. Variant chr3-191328981-G-A is described in ClinVar as [Benign]. Clinvar id is 1276371.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.233 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UTS2B	NM_198152.5	c.-664-272C>T		intron_variant		ENST00000340524.10
UTS2B	XM_011512631.3	c.-438C>T		5_prime_UTR_variant	1/8
UTS2B	XM_017006091.2	c.-438C>T		5_prime_UTR_variant	1/8
UTS2B	XM_047447899.1	c.-260-272C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UTS2B	ENST00000340524.10	c.-664-272C>T		intron_variant		2	NM_198152.5	P1
UTS2B	ENST00000432514.5	c.-831-272C>T		intron_variant		5
UTS2B	ENST00000464814.1	n.332C>T		non_coding_transcript_exon_variant	1/2	5
UTS2B	ENST00000490825.1	n.240-9C>T		splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26425 AN: 151984 Hom.: 2887 Cov.: 32

Gnomad AFR AF: 0.0585

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.190

GnomAD4 exome AF: 0.217 AC: 13 AN: 60 Hom.: 2 Cov.: 0 AF XY: 0.143 AC XY: 6 AN XY: 42

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.400

Gnomad4 NFE exome AF: 0.237

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.174 AC: 26438 AN: 152102 Hom.: 2888 Cov.: 32 AF XY: 0.173 AC XY: 12893 AN XY: 74354

Gnomad4 AFR AF: 0.0586

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.243

Gnomad4 EAS AF: 0.00213

Gnomad4 SAS AF: 0.115

Gnomad4 FIN AF: 0.250

Gnomad4 NFE AF: 0.236

Gnomad4 OTH AF: 0.186

Alfa AF: 0.210 Hom.: 772

Bravo AF: 0.168

Asia WGS AF: 0.0620 AC: 214 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 07, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.20
DANN	Benign	0.66

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: rs4687210; hg19: chr3-191046770;