Variant 5-152395503-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_020167.5(NMUR2):c.893G>C(p.Ser298Thr) variant causes a missense change. The variant allele was found at a frequency of 0.18 in 1,612,954 control chromosomes in the GnomAD database, including 28,613 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.

Frequency

Genomes: 𝑓 0.14 ( 2080 hom., cov: 30)

Exomes 𝑓: 0.18 ( 26533 hom. )

Consequence

NMUR2
NM_020167.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.20

Variant links:

Genes affected

NMUR2 (HGNC:16454): (neuromedin U receptor 2) This gene encodes a protein from the G-protein coupled receptor 1 family. This protein is a receptor for neuromedin U, which is a neuropeptide that is widely distributed in the gut and central nervous system. This receptor plays an important role in the regulation of food intake and body weight. [provided by RefSeq, Jul 2008]

NMUR2 links:

ENSG00000286749 (HGNC:):

ENSG00000286749 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.00396955).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NMUR2	NM_020167.5 link	c.893G>C	p.Ser298Thr	missense_variant	3/4	ENST00000255262.4	NP_064552.3	Q9GZQ4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
NMUR2	ENST00000255262.4 link	c.893G>C	p.Ser298Thr	missense_variant	3/4	1	NM_020167.5	ENSP00000255262.4	Q9GZQ4
NMUR2	ENST00000518933.1 link	n.439G>C		non_coding_transcript_exon_variant	4/4	3
ENSG00000286749	ENST00000663460.1 link	n.216+20290C>G		intron_variant
ENSG00000286749	ENST00000663819.1 link	n.183+20290C>G		intron_variant

Frequencies

GnomAD3 genomes

AF:

0.145

AC:

21974

AN:

151722

Hom.:

2083

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0422

Gnomad AMI

AF:

0.149

Gnomad AMR

AF:

0.237

Gnomad ASJ

AF:

0.153

Gnomad EAS

AF:

0.0345

Gnomad SAS

AF:

0.177

Gnomad FIN

AF:

0.182

Gnomad MID

AF:

0.168

Gnomad NFE

AF:

0.186

Gnomad OTH

AF:

0.145

GnomAD3 exomes

AF:

0.183

AC:

45986

AN:

250910

Hom.:

5346

AF XY:

0.182

AC XY:

24647

AN XY:

135596

show subpopulations

Gnomad AFR exome

AF:

0.0415

Gnomad AMR exome

AF:

0.350

Gnomad ASJ exome

AF:

0.154

Gnomad EAS exome

AF:

0.0317

Gnomad SAS exome

AF:

0.190

Gnomad FIN exome

AF:

0.175

Gnomad NFE exome

AF:

0.180

Gnomad OTH exome

AF:

0.172

GnomAD4 exome

AF:

0.183

AC:

267914

AN:

1461114

Hom.:

26533

Cov.:

AF XY:

0.183

AC XY:

133010

AN XY:

726870

show subpopulations

Gnomad4 AFR exome

AF:

0.0382

Gnomad4 AMR exome

AF:

0.339

Gnomad4 ASJ exome

AF:

0.157

Gnomad4 EAS exome

AF:

0.0232

Gnomad4 SAS exome

AF:

0.192

Gnomad4 FIN exome

AF:

0.179

Gnomad4 NFE exome

AF:

0.188

Gnomad4 OTH exome

AF:

0.169

GnomAD4 genome

AF:

0.145

AC:

21963

AN:

151840

Hom.:

2080

Cov.:

AF XY:

0.145

AC XY:

10776

AN XY:

74158

show subpopulations

Gnomad4 AFR

AF:

0.0422

Gnomad4 AMR

AF:

0.237

Gnomad4 ASJ

AF:

0.153

Gnomad4 EAS

AF:

0.0346

Gnomad4 SAS

AF:

0.176

Gnomad4 FIN

AF:

0.182

Gnomad4 NFE

AF:

0.186

Gnomad4 OTH

AF:

0.143

Alfa

AF:

0.162

Hom.:

1638

Bravo

AF:

0.147

TwinsUK

AF:

0.205

AC:

759

ALSPAC

AF:

0.193

AC:

744

ESP6500AA

AF:

0.0531

AC:

234

ESP6500EA

AF:

0.181

AC:

1556

ExAC

AF:

0.174

AC:

21179

Asia WGS

AF:

0.0850

AC:

297

AN:

3478

EpiCase

AF:

0.186

EpiControl

AF:

0.176

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.057

BayesDel_addAF

Benign

-0.68

BayesDel_noAF

Benign

-0.61

CADD

Benign

DANN

Benign

0.22

DEOGEN2

Benign

0.016

Eigen

Benign

-0.89

Eigen_PC

Benign

-0.63

FATHMM_MKL

Benign

0.052

LIST_S2

Benign

0.056

MetaRNN

Benign

0.0040

MetaSVM

Benign

-1.0

MutationAssessor

Benign

-1.4

PrimateAI

Uncertain

0.55

PROVEAN

Benign

2.7

REVEL

Benign

0.15

Sift

Benign

1.0

Sift4G

Benign

1.0

Polyphen

0.0

Vest4

0.028

MPC

0.13

ClinPred

0.0074

GERP RS

3.0

Varity_R

0.044

gMVP

0.37

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over