NM_198152.5:c.53C>T

Variant names:

• chr3-191282137-G-A
• rs190479512
• NM_198152.5:c.53C>T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_198152.5(UTS2B):​c.53C>T​(p.Ser18Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: UTS2B NM_198152.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.48

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 Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.1434227).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UTS2B	NM_198152.5	c.53C>T	p.Ser18Phe	missense_variant	Exon 5 of 9	ENST00000340524.10	NP_937795.2
UTS2B	XM_017006091.2	c.53C>T	p.Ser18Phe	missense_variant	Exon 4 of 8		XP_016861580.1
UTS2B	XM_011512631.3	c.53C>T	p.Ser18Phe	missense_variant	Exon 4 of 8		XP_011510933.1
UTS2B	XM_047447899.1	c.53C>T	p.Ser18Phe	missense_variant	Exon 4 of 8		XP_047303855.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UTS2B	ENST00000340524.10	c.53C>T	p.Ser18Phe	missense_variant	Exon 5 of 9	2	NM_198152.5	ENSP00000340526.5

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 34

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.11
BayesDel_addAF	Benign	-0.019	T
BayesDel_noAF	Benign	-0.26
CADD	Benign	15
DANN	Uncertain	0.99
DEOGEN2	Benign	0.097	T;T;.
Eigen	Benign	-0.67
Eigen_PC	Benign	-0.70
FATHMM_MKL	Benign	0.12	N
LIST_S2	Benign	0.52	.;T;T
M_CAP	Benign	0.036	D
MetaRNN	Benign	0.14	T;T;T
MetaSVM	Benign	-0.86	T
MutationAssessor	Benign	2.0	M;M;.
PrimateAI	Benign	0.33	T
PROVEAN	Benign	-2.2	N;N;D
REVEL	Benign	0.21
Sift	Benign	0.11	T;T;D
Sift4G	Benign	0.13	T;T;D
Polyphen		0.11	B;B;.
Vest4		0.32
MutPred		0.41		Gain of catalytic residue at S21 (P = 0.4212);Gain of catalytic residue at S21 (P = 0.4212);Gain of catalytic residue at S21 (P = 0.4212);
MVP		0.49
MPC		0.21
ClinPred		0.24	T
GERP RS		4.0
Varity_R		0.079
gMVP		0.41

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs190479512; hg19: chr3-190999926;