Genetic Variant NTSR2:p.Arg64Arg (chr2-11669938-G-T) – ACMG Classification: Benign (-11 pts)

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_012344.4(NTSR2):c.192C>A(p.Arg64Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00191 in 1,518,268 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0012 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0020 ( 6 hom. )

Consequence

NTSR2
NM_012344.4 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.75

Variant links:

Genes affected

NTSR2 (HGNC:8040): (neurotensin receptor 2) The protein encoded by this gene belongs to the G protein-coupled receptor family that activate a phosphatidylinositol-calcium second messenger system. Binding and pharmacological studies demonstrate that this receptor binds neurotensin as well as several other ligands already described for neurotensin NT1 receptor. However, unlike NT1 receptor, this gene recognizes, with high affinity, levocabastine, a histamine H1 receptor antagonist previously shown to compete with neurotensin for low-affinity binding sites in brain. These activities suggest that this receptor may be of physiological importance and that a natural agonist for the receptor may exist. [provided by RefSeq, Jul 2008]

NTSR2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.55).

BP6

Variant 2-11669938-G-T is Benign according to our data. Variant chr2-11669938-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 2650687.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=2.75 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 6 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NTSR2	NM_012344.4 link	c.192C>A	p.Arg64Arg	synonymous_variant	Exon 1 of 4	ENST00000306928.6	NP_036476.2	O95665

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NTSR2	ENST00000306928.6 link	c.192C>A	p.Arg64Arg	synonymous_variant	Exon 1 of 4	1	NM_012344.4	ENSP00000303686.5		O95665

Frequencies

GnomAD3 genomes

AF:

0.00120

AC:

182

AN:

152176

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000241

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000851

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000188

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00226

Gnomad OTH

AF:

0.00143

GnomAD2 exomes

AF:

0.00135

AC:

154

AN:

114318

AF XY:

0.00138

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.000871

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.000287

Gnomad NFE exome

AF:

0.00281

Gnomad OTH exome

AF:

0.00205

GnomAD4 exome

AF:

0.00199

AC:

2714

AN:

1366092

Hom.:

Cov.:

AF XY:

0.00191

AC XY:

1291

AN XY:

674286

show subpopulations

Gnomad4 AFR exome

AF:

0.000340

AC:

AN:

29416

Gnomad4 AMR exome

AF:

0.000579

AC:

AN:

31086

Gnomad4 ASJ exome

AF:

0.0000424

AC:

AN:

23586

Gnomad4 EAS exome

AF:

0.00

AC:

AN:

35146

Gnomad4 SAS exome

AF:

0.0000263

AC:

AN:

75988

Gnomad4 FIN exome

AF:

0.000610

AC:

AN:

37694

Gnomad4 NFE exome

AF:

0.00239

AC:

2565

AN:

1072038

Gnomad4 Remaining exome

AF:

0.00167

AC:

AN:

56762

Heterozygous variant carriers

193

386

579

772

965

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Exome Het

Exome Hom

Variant carriers

192

288

384

480

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00120

AC:

182

AN:

152176

Hom.:

Cov.:

AF XY:

0.00109

AC XY:

AN XY:

74350

show subpopulations

Gnomad4 AFR

AF:

0.000241

AC:

0.000241266

AN:

0.000241266

Gnomad4 AMR

AF:

0.000851

AC:

0.000850563

AN:

0.000850563

Gnomad4 ASJ

AF:

0.00

AC:

AN:

Gnomad4 EAS

AF:

0.00

AC:

AN:

Gnomad4 SAS

AF:

0.00

AC:

AN:

Gnomad4 FIN

AF:

0.000188

AC:

0.000188466

AN:

0.000188466

Gnomad4 NFE

AF:

0.00226

AC:

0.00226391

AN:

0.00226391

Gnomad4 OTH

AF:

0.00143

AC:

0.00143403

AN:

0.00143403

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.000831

Hom.:

Bravo

AF:

0.00117

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Jul 01, 2022

CeGaT Center for Human Genetics Tuebingen

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

NTSR2: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.55

CADD

Benign

3.9

DANN

Benign

0.71

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

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