chr3-191328956-C-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

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

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.769
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

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
UTS2BNM_198152.5 linkuse as main transcriptc.-664-247G>A intron_variant ENST00000340524.10 NP_937795.2
UTS2BXM_011512631.3 linkuse as main transcriptc.-413G>A 5_prime_UTR_variant 1/8 XP_011510933.1
UTS2BXM_017006091.2 linkuse as main transcriptc.-413G>A 5_prime_UTR_variant 1/8 XP_016861580.1
UTS2BXM_047447899.1 linkuse as main transcriptc.-260-247G>A intron_variant XP_047303855.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
UTS2BENST00000340524.10 linkuse as main transcriptc.-664-247G>A intron_variant 2 NM_198152.5 ENSP00000340526 P1
UTS2BENST00000432514.5 linkuse as main transcriptc.-831-247G>A intron_variant 5 ENSP00000401028
UTS2BENST00000464814.1 linkuse as main transcriptn.357G>A non_coding_transcript_exon_variant 1/25
UTS2BENST00000490825.1 linkuse as main transcriptn.256G>A non_coding_transcript_exon_variant 2/45

Frequencies

GnomAD3 genomes
AF:
0.0602
AC:
9157
AN:
152090
Hom.:
429
Cov.:
32
show subpopulations
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
show subpopulations
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
show subpopulations
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
LINK: link

Submissions by phenotype

not provided Benign:2
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Benign, criteria provided, single submitterclinical testingGeneDxApr 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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs62617841; hg19: chr3-191046745; API