3-191278152-T-A

Variant names:

• chr3-191278152-T-A
• rs1482786039
• NM_198152.5:c.122A>T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_198152.5(UTS2B):​c.122A>T​(p.Asp41Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000072 in 1,388,810 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D41A) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 7.2e-7 (0 hom.)
• Consequence: UTS2B NM_198152.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.335
• Publications: 0 publications found

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

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.18499705).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_198152.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UTS2B	NM_198152.5	MANE Select	c.122A>T	p.Asp41Val	missense	Exon 6 of 9	NP_937795.2	Q765I0

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UTS2B	ENST00000340524.10	TSL:2 MANE Select	c.122A>T	p.Asp41Val	missense	Exon 6 of 9	ENSP00000340526.5	Q765I0
	UTS2B	ENST00000427544.6	TSL:1	c.122A>T	p.Asp41Val	missense	Exon 2 of 5	ENSP00000398761.2	Q765I0
	UTS2B	ENST00000899455.1		c.122A>T	p.Asp41Val	missense	Exon 5 of 8	ENSP00000569514.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 7.20e-7 AC: 1 AN: 1388810 Hom.: 0 Cov.: 25 AF XY: 0.00000145 AC XY: 1 AN XY: 691258

African (AFR) AF: 0.00 AC: 0 AN: 30106

American (AMR) AF: 0.00 AC: 0 AN: 30770

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 24020

East Asian (EAS) AF: 0.00 AC: 0 AN: 37756

South Asian (SAS) AF: 0.0000132 AC: 1 AN: 75982

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 51960

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5568

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1075500

Other (OTH) AF: 0.00 AC: 0 AN: 57148

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.12
BayesDel_addAF	Benign	-0.11	T
BayesDel_noAF	Benign	-0.39
CADD	Benign	11
DANN	Benign	0.88
DEOGEN2	Benign	0.072	T
Eigen	Benign	-0.26
Eigen_PC	Benign	-0.40
FATHMM_MKL	Benign	0.15	N
LIST_S2	Benign	0.51	T
M_CAP	Benign	0.023	T
MetaRNN	Benign	0.18	T
MetaSVM	Benign	-0.85	T
MutationAssessor	Benign	1.8	L
PhyloP100		0.34
PrimateAI	Benign	0.29	T
PROVEAN	Uncertain	-4.0	D
REVEL	Benign	0.11
Sift	Benign	0.037	D
Sift4G	Benign	0.16	T
Polyphen		0.93	P
Vest4		0.26
MutPred		0.32		Loss of solvent accessibility (P = 0.0159)
MVP		0.12
MPC		0.16
ClinPred		0.39	T
GERP RS		1.9
Varity_R		0.13
gMVP		0.16
Mutation Taster		=82/18	polymorphism

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

Other links and lift over

dbSNP: rs1482786039; hg19: chr3-190995941;