Variant 20-62709422-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_002531.3(NTSR1):c.215C>T(p.Ala72Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00976 in 1,611,788 control chromosomes in the GnomAD database, including 105 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.0063 ( 7 hom., cov: 33)

Exomes 𝑓: 0.010 ( 98 hom. )

Consequence

NTSR1
NM_002531.3 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0440

Variant links:

Genes affected

NTSR1 (HGNC:8039): (neurotensin receptor 1) Neurotensin receptor 1 belongs to the large superfamily of G-protein coupled receptors. NTSR1 mediates the multiple functions of neurotensin, such as hypotension, hyperglycemia, hypothermia, antinociception, and regulation of intestinal motility and secretion. [provided by RefSeq, Jul 2008]

NTSR1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0048886836).

BP6

Variant 20-62709422-C-T is Benign according to our data. Variant chr20-62709422-C-T is described in ClinVar as [Benign]. Clinvar id is 708255.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd at 7 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NTSR1	NM_002531.3 linkuse as main transcript	c.215C>T	p.Ala72Val	missense_variant	1/4	ENST00000370501.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NTSR1	ENST00000370501.4 linkuse as main transcript	c.215C>T	p.Ala72Val	missense_variant	1/4	1	NM_002531.3	P1

Frequencies

GnomAD3 genomes

AF:

0.00633

AC:

963

AN:

152244

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00217

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00242

Gnomad ASJ

AF:

0.00375

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00165

Gnomad FIN

AF:

0.00433

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0112

Gnomad OTH

AF:

0.00478

GnomAD3 exomes

AF:

0.00617

AC:

1532

AN:

248196

Hom.:

AF XY:

0.00622

AC XY:

838

AN XY:

134664

show subpopulations

Gnomad AFR exome

AF:

0.00168

Gnomad AMR exome

AF:

0.00159

Gnomad ASJ exome

AF:

0.00232

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00246

Gnomad FIN exome

AF:

0.00472

Gnomad NFE exome

AF:

0.0109

Gnomad OTH exome

AF:

0.00578

GnomAD4 exome

AF:

0.0101

AC:

14771

AN:

1459426

Hom.:

Cov.:

AF XY:

0.00988

AC XY:

7168

AN XY:

725848

show subpopulations

Gnomad4 AFR exome

AF:

0.00140

Gnomad4 AMR exome

AF:

0.00172

Gnomad4 ASJ exome

AF:

0.00276

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00225

Gnomad4 FIN exome

AF:

0.00502

Gnomad4 NFE exome

AF:

0.0123

Gnomad4 OTH exome

AF:

0.00766

GnomAD4 genome

AF:

0.00633

AC:

964

AN:

152362

Hom.:

Cov.:

AF XY:

0.00600

AC XY:

447

AN XY:

74508

show subpopulations

Gnomad4 AFR

AF:

0.00216

Gnomad4 AMR

AF:

0.00242

Gnomad4 ASJ

AF:

0.00375

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00186

Gnomad4 FIN

AF:

0.00433

Gnomad4 NFE

AF:

0.0112

Gnomad4 OTH

AF:

0.00473

Alfa

AF:

0.0104

Hom.:

Bravo

AF:

0.00654

TwinsUK

AF:

0.00782

AC:

ALSPAC

AF:

0.0114

AC:

ESP6500AA

AF:

0.00182

AC:

ESP6500EA

AF:

0.0113

AC:

ExAC

AF:

0.00645

AC:

782

Asia WGS

AF:

0.000866

AC:

AN:

3478

EpiCase

AF:

0.00981

EpiControl

AF:

0.00967

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Mar 29, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.066

BayesDel_addAF

Benign

-0.63

BayesDel_noAF

Benign

-0.68

Cadd

Benign

Dann

Benign

0.97

DEOGEN2

Benign

0.059

Eigen

Benign

-0.75

Eigen_PC

Benign

-0.62

FATHMM_MKL

Benign

0.30

LIST_S2

Benign

0.74

MetaRNN

Benign

0.0049

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.97

MutationTaster

Benign

0.69

PrimateAI

Benign

0.41

PROVEAN

Benign

0.41

REVEL

Benign

0.030

Sift

Benign

1.0

Sift4G

Benign

0.53

Polyphen

0.12

Vest4

0.093

MVP

0.29

MPC

0.31

ClinPred

0.0040

GERP RS

3.4

Varity_R

0.14

gMVP

0.43

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