chr3-191329004-G-C

Position:

• chr3-191329004-G-C

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.-664-295C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.449 in 152,236 control chromosomes in the GnomAD database, including 18,686 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.45 (18678 hom., cov: 33)
  • Exomes 𝑓: 0.34 (8 hom.)
• Consequence: UTS2B NM_198152.5 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.952

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=-0.83).
• BP6: Variant 3-191329004-G-C is Benign according to our data. Variant chr3-191329004-G-C is described in ClinVar as [Benign]. Clinvar id is 1273417.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.895 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UTS2B	NM_198152.5	c.-664-295C>G		intron_variant		ENST00000340524.10	NP_937795.2
UTS2B	XM_011512631.3	c.-461C>G		5_prime_UTR_variant	1/8		XP_011510933.1
UTS2B	XM_017006091.2	c.-461C>G		5_prime_UTR_variant	1/8		XP_016861580.1
UTS2B	XM_047447899.1	c.-260-295C>G		intron_variant			XP_047303855.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UTS2B	ENST00000340524.10	c.-664-295C>G		intron_variant		2	NM_198152.5	ENSP00000340526	P1
UTS2B	ENST00000432514.5	c.-831-295C>G		intron_variant		5		ENSP00000401028
UTS2B	ENST00000464814.1	n.309C>G		non_coding_transcript_exon_variant	1/2	5
UTS2B	ENST00000490825.1	n.240-32C>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.449 AC: 68233 AN: 152024 Hom.: 18653 Cov.: 33

Gnomad AFR AF: 0.712

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.917

Gnomad SAS AF: 0.575

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.400

GnomAD4 exome AF: 0.340 AC: 32 AN: 94 Hom.: 8 Cov.: 0 AF XY: 0.348 AC XY: 23 AN XY: 66

Gnomad4 AFR exome AF: 0.667

Gnomad4 SAS exome AF: 0.750

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.286

Gnomad4 OTH exome AF: 0.833

GnomAD4 genome AF: 0.449 AC: 68305 AN: 152142 Hom.: 18678 Cov.: 33 AF XY: 0.456 AC XY: 33909 AN XY: 74386

Gnomad4 AFR AF: 0.712

Gnomad4 AMR AF: 0.467

Gnomad4 ASJ AF: 0.309

Gnomad4 EAS AF: 0.917

Gnomad4 SAS AF: 0.575

Gnomad4 FIN AF: 0.287

Gnomad4 NFE AF: 0.277

Gnomad4 OTH AF: 0.403

Alfa AF: 0.351 Hom.: 1403

Bravo AF: 0.473

Asia WGS AF: 0.729 AC: 2530 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	Nov 10, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.7
DANN	Benign	0.56

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: rs6779820; hg19: chr3-191046793;