5-152395503-C-G

Variant names:

• chr5-152395503-C-G
• rs4958535
• NM_020167.5:c.893G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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. 14/21 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: 30)
  • Exomes 𝑓: 0.18 (26533 hom.)
• Consequence: NMUR2 NM_020167.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.20
• Publications: 22 publications found

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]

ENSG00000286749 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020167.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NMUR2	NM_020167.5	MANE Select	c.893G>C	p.Ser298Thr	missense	Exon 3 of 4	NP_064552.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NMUR2	ENST00000255262.4	TSL:1 MANE Select	c.893G>C	p.Ser298Thr	missense	Exon 3 of 4	ENSP00000255262.4
	NMUR2	ENST00000518933.1	TSL:3	n.439G>C		non_coding_transcript_exon	Exon 4 of 4
	ENSG00000286749	ENST00000663460.1		n.216+20290C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.145 AC: 21974 AN: 151722 Hom.: 2083 Cov.: 30

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

GnomAD2 exomes AF: 0.183 AC: 45986 AN: 250910 AF XY: 0.182

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 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.: 33 AF XY: 0.183 AC XY: 133010 AN XY: 726870

African (AFR) AF: 0.0382 AC: 1277 AN: 33452

American (AMR) AF: 0.339 AC: 15153 AN: 44640

Ashkenazi Jewish (ASJ) AF: 0.157 AC: 4094 AN: 26118

East Asian (EAS) AF: 0.0232 AC: 920 AN: 39694

South Asian (SAS) AF: 0.192 AC: 16529 AN: 86218

European-Finnish (FIN) AF: 0.179 AC: 9557 AN: 53402

Middle Eastern (MID) AF: 0.136 AC: 780 AN: 5756

European-Non Finnish (NFE) AF: 0.188 AC: 209394 AN: 1111482

Other (OTH) AF: 0.169 AC: 10210 AN: 60352

GnomAD4 genome AF: 0.145 AC: 21963 AN: 151840 Hom.: 2080 Cov.: 30 AF XY: 0.145 AC XY: 10776 AN XY: 74158

African (AFR) AF: 0.0422 AC: 1747 AN: 41436

American (AMR) AF: 0.237 AC: 3608 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.153 AC: 532 AN: 3466

East Asian (EAS) AF: 0.0346 AC: 179 AN: 5172

South Asian (SAS) AF: 0.176 AC: 845 AN: 4794

European-Finnish (FIN) AF: 0.182 AC: 1911 AN: 10514

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12660 AN: 67922

Other (OTH) AF: 0.143 AC: 301 AN: 2104

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 v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.057
BayesDel_addAF	Benign	-0.68	T
BayesDel_noAF	Benign	-0.61
CADD	Benign	16
DANN	Benign	0.22
DEOGEN2	Benign	0.016	T
Eigen	Benign	-0.89
Eigen_PC	Benign	-0.63
FATHMM_MKL	Benign	0.052	N
LIST_S2	Benign	0.056	T
MetaRNN	Benign	0.0040	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	-1.4	N
PhyloP100		4.2
PrimateAI	Uncertain	0.55	T
PROVEAN	Benign	2.7	N
REVEL	Benign	0.15
Sift	Benign	1.0	T
Sift4G	Benign	1.0	T
Polyphen		0.0	B
Vest4		0.028
MPC		0.13
ClinPred		0.0074	T
GERP RS		3.0
Varity_R		0.044
gMVP		0.37
Mutation Taster		=97/3	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4958535; hg19: chr5-151775064; COSMIC: COSV54916853;