17-82374420-C-T

Variant names:

• chr17-82374420-C-T
• rs34668956
• NM_018949.3:c.96C>T

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_Strong BP6_Very_Strong BP7 BA1

The NM_018949.3(UTS2R):​c.96C>T​(p.Leu32Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00257 in 1,598,542 control chromosomes in the GnomAD database, including 102 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.014 (50 hom., cov: 33)
  • Exomes 𝑓: 0.0014 (52 hom.)
• Consequence: UTS2R NM_018949.3 synonymous
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 1.82
• 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 -21 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BP6: Variant 17-82374420-C-T is Benign according to our data. Variant chr17-82374420-C-T is described in ClinVar as Benign. ClinVar VariationId is 777260.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=1.83 with no splicing effect.
• BA1: GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0514 is higher than 0.05.

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.96C>T	p.Leu32Leu	synonymous	Exon 3 of 3	NP_061822.1	Q9UKP6
	UTS2R	NM_001381897.1		c.96C>T	p.Leu32Leu	synonymous	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.96C>T	p.Leu32Leu	synonymous	Exon 3 of 3	ENSP00000323516.2	Q9UKP6
	UTS2R	ENST00000856767.1		c.96C>T	p.Leu32Leu	synonymous	Exon 2 of 2	ENSP00000526826.1
	UTS2R	ENST00000923106.1		c.96C>T	p.Leu32Leu	synonymous	Exon 4 of 4	ENSP00000593165.1

Frequencies

GnomAD3 genomes AF: 0.0138 AC: 2097 AN: 152180 Hom.: 49 Cov.: 33

Gnomad AFR AF: 0.0487

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00366

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000147

Gnomad OTH AF: 0.0100

GnomAD2 exomes AF: 0.00341 AC: 741 AN: 217268 AF XY: 0.00249

Gnomad AFR exome AF: 0.0523

Gnomad AMR exome AF: 0.00116

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000104

Gnomad OTH exome AF: 0.00146

GnomAD4 exome AF: 0.00139 AC: 2010 AN: 1446244 Hom.: 52 Cov.: 32 AF XY: 0.00121 AC XY: 870 AN XY: 719208

African (AFR) AF: 0.0535 AC: 1783 AN: 33328

American (AMR) AF: 0.00145 AC: 63 AN: 43566

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25854

East Asian (EAS) AF: 0.00 AC: 0 AN: 39322

South Asian (SAS) AF: 0.0000118 AC: 1 AN: 84944

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 45028

Middle Eastern (MID) AF: 0.000348 AC: 2 AN: 5754

European-Non Finnish (NFE) AF: 0.0000135 AC: 15 AN: 1108534

Other (OTH) AF: 0.00244 AC: 146 AN: 59914

GnomAD4 genome AF: 0.0138 AC: 2098 AN: 152298 Hom.: 50 Cov.: 33 AF XY: 0.0129 AC XY: 959 AN XY: 74474

African (AFR) AF: 0.0486 AC: 2021 AN: 41558

American (AMR) AF: 0.00359 AC: 55 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5176

South Asian (SAS) AF: 0.00 AC: 0 AN: 4826

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10622

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0000147 AC: 1 AN: 68016

Other (OTH) AF: 0.00994 AC: 21 AN: 2112

Alfa AF: 0.00564 Hom.: 1

Bravo AF: 0.0158

Asia WGS AF: 0.00173 AC: 6 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.2
DANN	Benign	0.77
PhyloP100		1.8
Mutation Taster		=100/0	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: rs34668956; hg19: chr17-80332296;