Variant chr1-7847871-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate

The NM_006786.4(UTS2):c.270C>A(p.Phe90Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000253 in 1,607,122 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0013 ( 0 hom., cov: 32)

Exomes 𝑓: 0.00015 ( 1 hom. )

Consequence

UTS2
NM_006786.4 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.157

Variant links:

Genes affected

UTS2 (HGNC:12636): (urotensin 2) This gene encodes a mature peptide that is an active cyclic heptapeptide absolutely conserved from lamprey to human. The active peptide acts as a vasoconstrictor and is expressed only in brain tissue. Despite the gene family name similarity, this gene is not homologous to urocortin, a member of the sauvagine/corticotropin-releasing factor/urotensin I family. Most of the proprotein is cleaved to make the mature peptide. Transcript variants encoding different preproprotein isoforms have been described for this gene. [provided by RefSeq, Jul 2008]

UTS2 links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.0047192276).

BP6

Variant 1-7847871-G-T is Benign according to our data. Variant chr1-7847871-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 787203.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
UTS2	NM_006786.4 linkuse as main transcript	c.270C>A	p.Phe90Leu	missense_variant	4/4	ENST00000361696.10
UTS2	NM_021995.2 linkuse as main transcript	c.315C>A	p.Phe105Leu	missense_variant	5/5
UTS2	XM_011540537.3 linkuse as main transcript	c.315C>A	p.Phe105Leu	missense_variant	6/6
UTS2	XM_011540538.2 linkuse as main transcript	c.270C>A	p.Phe90Leu	missense_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UTS2	ENST00000361696.10 linkuse as main transcript	c.270C>A	p.Phe90Leu	missense_variant	4/4	1	NM_006786.4	P2	O95399-1
UTS2	ENST00000054668.5 linkuse as main transcript	c.315C>A	p.Phe105Leu	missense_variant	5/5	1		A2	O95399-2
UTS2	ENST00000377516.6 linkuse as main transcript	c.270C>A	p.Phe90Leu	missense_variant	5/7	5

Frequencies

GnomAD3 genomes

AF:

0.00126

AC:

190

AN:

151284

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00456

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000660

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.000480

GnomAD3 exomes

AF:

0.000318

AC:

AN:

245384

Hom.:

AF XY:

0.000279

AC XY:

AN XY:

132568

show subpopulations

Gnomad AFR exome

AF:

0.00480

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00000894

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.000148

AC:

216

AN:

1455720

Hom.:

Cov.:

AF XY:

0.000139

AC XY:

101

AN XY:

724176

show subpopulations

Gnomad4 AFR exome

AF:

0.00590

Gnomad4 AMR exome

AF:

0.0000683

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000270

Gnomad4 OTH exome

AF:

0.000249

GnomAD4 genome

AF:

0.00125

AC:

190

AN:

151402

Hom.:

Cov.:

AF XY:

0.00115

AC XY:

AN XY:

73950

show subpopulations

Gnomad4 AFR

AF:

0.00454

Gnomad4 AMR

AF:

0.0000659

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00

Gnomad4 OTH

AF:

0.000474

Alfa

AF:

0.000250

Hom.:

Bravo

AF:

0.00151

ESP6500AA

AF:

0.00318

AC:

ESP6500EA

AF:

0.00

AC:

ExAC

AF:

0.000354

AC:

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 submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jul 06, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.59

BayesDel_addAF

Benign

-0.60

BayesDel_noAF

Benign

-0.63

CADD

Benign

3.6

DANN

Benign

0.95

DEOGEN2

Benign

0.18

.;T;.

Eigen

Benign

-1.2

Eigen_PC

Benign

-1.1

FATHMM_MKL

Benign

0.10

LIST_S2

Benign

0.45

T;T;T

M_CAP

Benign

0.0072

MetaRNN

Benign

0.0047

T;T;T

MetaSVM

Benign

-0.99

MutationAssessor

Benign

0.69

.;N;.

MutationTaster

Benign

1.0

N;N;N

PrimateAI

Benign

0.34

PROVEAN

Pathogenic

-4.6

D;D;D

REVEL

Benign

0.017

Sift

Benign

0.098

T;T;T

Sift4G

Benign

0.34

T;T;T

Polyphen

0.0090

B;B;B

Vest4

0.23

MutPred

0.31

Gain of ubiquitination at K86 (P = 0.095);Gain of ubiquitination at K86 (P = 0.095);.;

MVP

0.10

MPC

0.27

ClinPred

0.025

GERP RS

0.38

Varity_R

0.13

gMVP

0.055

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over