chr3-191328941-T-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The NM_198152.5(UTS2B):​c.-664-232A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00552 in 152,310 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0055 ( 7 hom., cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

UTS2B
NM_198152.5 intron

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.30
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
Variant 3-191328941-T-C is Benign according to our data. Variant chr3-191328941-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 1190935.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00552 (841/152310) while in subpopulation AFR AF= 0.019 (789/41570). AF 95% confidence interval is 0.0179. There are 7 homozygotes in gnomad4. There are 410 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 7 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
UTS2BNM_198152.5 linkuse as main transcriptc.-664-232A>G intron_variant ENST00000340524.10 NP_937795.2
UTS2BXM_011512631.3 linkuse as main transcriptc.-398A>G 5_prime_UTR_variant 1/8 XP_011510933.1
UTS2BXM_017006091.2 linkuse as main transcriptc.-398A>G 5_prime_UTR_variant 1/8 XP_016861580.1
UTS2BXM_047447899.1 linkuse as main transcriptc.-260-232A>G intron_variant XP_047303855.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
UTS2BENST00000340524.10 linkuse as main transcriptc.-664-232A>G intron_variant 2 NM_198152.5 ENSP00000340526 P1
UTS2BENST00000432514.5 linkuse as main transcriptc.-831-232A>G intron_variant 5 ENSP00000401028
UTS2BENST00000464814.1 linkuse as main transcriptn.372A>G non_coding_transcript_exon_variant 1/25
UTS2BENST00000490825.1 linkuse as main transcriptn.271A>G non_coding_transcript_exon_variant 2/45

Frequencies

GnomAD3 genomes
AF:
0.00540
AC:
822
AN:
152192
Hom.:
6
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0186
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00248
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000735
Gnomad OTH
AF:
0.00383
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
62
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
40
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.00552
AC:
841
AN:
152310
Hom.:
7
Cov.:
32
AF XY:
0.00550
AC XY:
410
AN XY:
74484
show subpopulations
Gnomad4 AFR
AF:
0.0190
Gnomad4 AMR
AF:
0.00248
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000735
Gnomad4 OTH
AF:
0.00379
Alfa
AF:
0.00451
Hom.:
0
Bravo
AF:
0.00640
Asia WGS
AF:
0.00606
AC:
21
AN:
3478

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingGeneDxMar 31, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
1.3
DANN
Benign
0.69

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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: rs112724649; hg19: chr3-191046730; API