17-82375058-C-T

Variant names:

• chr17-82375058-C-T
• rs199914220
• NM_018949.3:c.734C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Strong BP6_Moderate BS2

The NM_018949.3(UTS2R):​c.734C>T​(p.Ser245Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000995 in 1,421,024 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0015 (2 hom., cov: 33)
  • Exomes 𝑓: 0.00093 (9 hom.)
• Consequence: UTS2R NM_018949.3 missense
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.423
• Publications: 1 publications found

Genes affected

UTS2R (HGNC:4468): (urotensin 2 receptor) Predicted to enable urotensin II receptor activity. Predicted to be involved in neuropeptide signaling pathway. Predicted to be located in plasma membrane. Predicted to be integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.00550133).
• BP6: Variant 17-82375058-C-T is Benign according to our data. Variant chr17-82375058-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 2648495.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAd4 at 2 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018949.3. 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
	UTS2R	NM_018949.3	MANE Select	c.734C>T	p.Ser245Phe	missense	Exon 3 of 3	NP_061822.1	Q9UKP6
	UTS2R	NM_001381897.1		c.734C>T	p.Ser245Phe	missense	Exon 2 of 2	NP_001368826.1	Q9UKP6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UTS2R	ENST00000313135.5	TSL:6 MANE Select	c.734C>T	p.Ser245Phe	missense	Exon 3 of 3	ENSP00000323516.2	Q9UKP6
	UTS2R	ENST00000856767.1		c.734C>T	p.Ser245Phe	missense	Exon 2 of 2	ENSP00000526826.1
	UTS2R	ENST00000923106.1		c.734C>T	p.Ser245Phe	missense	Exon 4 of 4	ENSP00000593165.1

Frequencies

GnomAD3 genomes AF: 0.00155 AC: 235 AN: 151922 Hom.: 2 Cov.: 33

Gnomad AFR AF: 0.000990

Gnomad AMI AF: 0.00881

Gnomad AMR AF: 0.00550

Gnomad ASJ AF: 0.0104

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0192

Gnomad NFE AF: 0.000780

Gnomad OTH AF: 0.00335

GnomAD2 exomes AF: 0.00186 AC: 96 AN: 51630 AF XY: 0.00174

Gnomad AFR exome AF: 0.000942

Gnomad AMR exome AF: 0.00357

Gnomad ASJ exome AF: 0.0102

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000825

Gnomad OTH exome AF: 0.00565

GnomAD4 exome AF: 0.000929 AC: 1179 AN: 1268994 Hom.: 9 Cov.: 30 AF XY: 0.000987 AC XY: 617 AN XY: 624984

African (AFR) AF: 0.00123 AC: 31 AN: 25134

American (AMR) AF: 0.00599 AC: 94 AN: 15700

Ashkenazi Jewish (ASJ) AF: 0.0109 AC: 223 AN: 20408

East Asian (EAS) AF: 0.00 AC: 0 AN: 28420

South Asian (SAS) AF: 0.000693 AC: 43 AN: 62022

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 34200

Middle Eastern (MID) AF: 0.0110 AC: 49 AN: 4452

European-Non Finnish (NFE) AF: 0.000566 AC: 581 AN: 1026286

Other (OTH) AF: 0.00302 AC: 158 AN: 52372

GnomAD4 genome AF: 0.00155 AC: 235 AN: 152030 Hom.: 2 Cov.: 33 AF XY: 0.00159 AC XY: 118 AN XY: 74326

African (AFR) AF: 0.000988 AC: 41 AN: 41512

American (AMR) AF: 0.00550 AC: 84 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0104 AC: 36 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5164

South Asian (SAS) AF: 0.00 AC: 0 AN: 4828

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10530

Middle Eastern (MID) AF: 0.0207 AC: 6 AN: 290

European-Non Finnish (NFE) AF: 0.000780 AC: 53 AN: 67934

Other (OTH) AF: 0.00331 AC: 7 AN: 2112

Alfa AF: 0.00132 Hom.: 0

Bravo AF: 0.00244

TwinsUK AF: 0.000539 AC: 2

ALSPAC AF: 0.000519 AC: 2

ExAC AF: 0.000835 AC: 76

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.23
BayesDel_addAF	Benign	-0.50	T
BayesDel_noAF	Benign	-0.50
CADD	Benign	19
DANN	Benign	0.94
DEOGEN2	Uncertain	0.45	T
Eigen	Benign	-0.19
Eigen_PC	Benign	-0.42
FATHMM_MKL	Benign	0.33	N
LIST_S2	Benign	0.48	T
M_CAP	Uncertain	0.12	D
MetaRNN	Benign	0.0055	T
MetaSVM	Benign	-0.54	T
MutationAssessor	Benign	1.7	L
PhyloP100		0.42
PrimateAI	Uncertain	0.70	T
PROVEAN	Benign	-2.3	N
REVEL	Benign	0.19
Sift	Benign	0.28	T
Sift4G	Benign	0.41	T
Polyphen		0.98	D
Vest4		0.19
MVP		0.72
MPC		0.52
ClinPred		0.027	T
GERP RS		2.8
Varity_R		0.10
gMVP		0.22
Mutation Taster		=87/13	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: rs199914220; hg19: chr17-80332934;