dbSNP rs4958531: NMUR2:p.Met388Val (chr5-152392277-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_020167.5(NMUR2):c.1162A>G(p.Met388Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 1,613,544 control chromosomes in the GnomAD database, including 28,634 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.14 ( 2080 hom., cov: 32)

Exomes 𝑓: 0.18 ( 26554 hom. )

Consequence

NMUR2
NM_020167.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.471

Publications

19 publications found

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 was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0015337467).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.231 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NMUR2	NM_020167.5 link	c.1162A>G	p.Met388Val	missense_variant	Exon 4 of 4	ENST00000255262.4	NP_064552.3	Q9GZQ4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NMUR2	ENST00000255262.4 link	c.1162A>G	p.Met388Val	missense_variant	Exon 4 of 4	1	NM_020167.5	ENSP00000255262.4		Q9GZQ4

Frequencies

GnomAD3 genomes

AF:

0.145

AC:

22034

AN:

151998

Hom.:

2083

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0423

Gnomad AMI

AF:

0.148

Gnomad AMR

AF:

0.237

Gnomad ASJ

AF:

0.154

Gnomad EAS

AF:

0.0347

Gnomad SAS

AF:

0.177

Gnomad FIN

AF:

0.182

Gnomad MID

AF:

0.168

Gnomad NFE

AF:

0.187

Gnomad OTH

AF:

0.144

GnomAD2 exomes

AF:

0.184

AC:

46119

AN:

251328

AF XY:

0.182

show subpopulations

Gnomad AFR exome

AF:

0.0417

Gnomad AMR exome

AF:

0.350

Gnomad ASJ exome

AF:

0.154

Gnomad EAS exome

AF:

0.0318

Gnomad FIN exome

AF:

0.175

Gnomad NFE exome

AF:

0.181

Gnomad OTH exome

AF:

0.173

GnomAD4 exome

AF:

0.183

AC:

268060

AN:

1461428

Hom.:

26554

Cov.:

AF XY:

0.183

AC XY:

133079

AN XY:

727014

show subpopulations

African (AFR)

AF:

0.0383

AC:

1280

AN:

33458

American (AMR)

AF:

0.340

AC:

15177

AN:

44684

Ashkenazi Jewish (ASJ)

AF:

0.157

AC:

4097

AN:

26128

East Asian (EAS)

AF:

0.0232

AC:

921

AN:

39700

South Asian (SAS)

AF:

0.192

AC:

16545

AN:

86250

European-Finnish (FIN)

AF:

0.179

AC:

9566

AN:

53420

Middle Eastern (MID)

AF:

0.136

AC:

784

AN:

5764

European-Non Finnish (NFE)

AF:

0.188

AC:

209467

AN:

1111644

Other (OTH)

AF:

0.169

AC:

10223

AN:

60380

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.470

Heterozygous variant carriers

11806

23612

35418

47224

59030

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

7368

14736

22104

29472

36840

<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:

0.145

AC:

22023

AN:

152116

Hom.:

2080

Cov.:

AF XY:

0.145

AC XY:

10820

AN XY:

74368

show subpopulations

African (AFR)

AF:

0.0422

AC:

1753

AN:

41524

American (AMR)

AF:

0.237

AC:

3623

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.154

AC:

533

AN:

3468

East Asian (EAS)

AF:

0.0348

AC:

180

AN:

5172

South Asian (SAS)

AF:

0.177

AC:

850

AN:

4808

European-Finnish (FIN)

AF:

0.182

AC:

1925

AN:

10576

Middle Eastern (MID)

AF:

0.153

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.187

AC:

12679

AN:

67976

Other (OTH)

AF:

0.142

AC:

300

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

922

1844

2767

3689

4611

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

250

500

750

1000

1250

<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:

0.170

Hom.:

9923

Bravo

AF:

0.147

TwinsUK

AF:

0.204

AC:

757

ALSPAC

AF:

0.193

AC:

743

ESP6500AA

AF:

0.0533

AC:

235

ESP6500EA

AF:

0.181

AC:

1556

ExAC

AF:

0.174

AC:

21190

Asia WGS

AF:

0.0850

AC:

297

AN:

3478

EpiCase

AF:

0.187

EpiControl

AF:

0.177

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.055

BayesDel_addAF

Benign

-0.76

BayesDel_noAF

Benign

-0.71

CADD

Benign

0.0010

(source)

DANN

Benign

0.20

DEOGEN2

Benign

0.014

Eigen

Benign

-2.4

Eigen_PC

Benign

-2.4

FATHMM_MKL

Benign

0.014

LIST_S2

Benign

0.17

MetaRNN

Benign

0.0015

MetaSVM

Benign

-1.1

MutationAssessor

Benign

-1.3

PhyloP100

-0.47

PrimateAI

Benign

0.21

PROVEAN

Benign

0.60

REVEL

Benign

0.047

Sift

Benign

1.0

Sift4G

Benign

1.0

Polyphen

0.0

Vest4

0.011

MPC

0.15

ClinPred

0.00071

GERP RS

-7.2

Varity_R

0.034

gMVP

0.31

Mutation Taster

=99/1

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over