chr3-191328981-G-A

Variant summary

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

The NM_198152.5(UTS2B):​c.-664-272C>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

Scores

2

Clinical Significance

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

Conservation

PhyloP100: -2.47
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=-0.82).
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 Protein UniProt
UTS2BNM_198152.5 linkuse as main transcriptc.-664-272C>T intron_variant ENST00000340524.10 NP_937795.2
UTS2BXM_011512631.3 linkuse as main transcriptc.-438C>T 5_prime_UTR_variant 1/8 XP_011510933.1
UTS2BXM_017006091.2 linkuse as main transcriptc.-438C>T 5_prime_UTR_variant 1/8 XP_016861580.1
UTS2BXM_047447899.1 linkuse as main transcriptc.-260-272C>T intron_variant XP_047303855.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
UTS2BENST00000340524.10 linkuse as main transcriptc.-664-272C>T intron_variant 2 NM_198152.5 ENSP00000340526 P1
UTS2BENST00000432514.5 linkuse as main transcriptc.-831-272C>T intron_variant 5 ENSP00000401028
UTS2BENST00000464814.1 linkuse as main transcriptn.332C>T non_coding_transcript_exon_variant 1/25
UTS2BENST00000490825.1 linkuse as main transcriptn.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
show subpopulations
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
show subpopulations
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
show subpopulations
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
LINK: link

Submissions by phenotype

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

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

Other links and lift over

dbSNP: rs4687210; hg19: chr3-191046770; API