5-152392494-G-T

Variant names:

• chr5-152392494-G-T
• rs1895245
• NM_020167.5:c.945C>A

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_020167.5(NMUR2):​c.945C>A​(p.Phe315Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 1,609,094 control chromosomes in the GnomAD database, including 28,565 homozygotes. In-silico tool predicts 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 (2087 hom., cov: 32)
  • Exomes 𝑓: 0.18 (26478 hom.)
• Consequence: NMUR2 NM_020167.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.55
• Publications: 19 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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.231 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.945C>A	p.Phe315Leu	missense	Exon 4 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.945C>A	p.Phe315Leu	missense	Exon 4 of 4	ENSP00000255262.4
	ENSG00000286749	ENST00000663460.1		n.216+17281G>T		intron	N/A
	ENSG00000286749	ENST00000663819.1		n.183+17281G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.145 AC: 22042 AN: 152046 Hom.: 2090 Cov.: 32

Gnomad AFR AF: 0.0423

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.0345

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: 45861 AN: 249682 AF XY: 0.182

Gnomad AFR exome AF: 0.0417

Gnomad AMR exome AF: 0.351

Gnomad ASJ exome AF: 0.154

Gnomad EAS exome AF: 0.0318

Gnomad FIN exome AF: 0.176

Gnomad NFE exome AF: 0.181

Gnomad OTH exome AF: 0.173

GnomAD4 exome AF: 0.183 AC: 266695 AN: 1456930 Hom.: 26478 Cov.: 34 AF XY: 0.183 AC XY: 132381 AN XY: 724466

African (AFR) AF: 0.0382 AC: 1275 AN: 33394

American (AMR) AF: 0.340 AC: 15153 AN: 44576

Ashkenazi Jewish (ASJ) AF: 0.157 AC: 4074 AN: 26020

East Asian (EAS) AF: 0.0232 AC: 918 AN: 39652

South Asian (SAS) AF: 0.192 AC: 16503 AN: 86022

European-Finnish (FIN) AF: 0.179 AC: 9552 AN: 53308

Middle Eastern (MID) AF: 0.136 AC: 783 AN: 5746

European-Non Finnish (NFE) AF: 0.188 AC: 208264 AN: 1108000

Other (OTH) AF: 0.169 AC: 10173 AN: 60212

GnomAD4 genome AF: 0.145 AC: 22031 AN: 152164 Hom.: 2087 Cov.: 32 AF XY: 0.145 AC XY: 10821 AN XY: 74402

African (AFR) AF: 0.0423 AC: 1756 AN: 41556

American (AMR) AF: 0.237 AC: 3621 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 535 AN: 3472

East Asian (EAS) AF: 0.0346 AC: 179 AN: 5174

South Asian (SAS) AF: 0.176 AC: 851 AN: 4826

European-Finnish (FIN) AF: 0.182 AC: 1933 AN: 10592

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

European-Non Finnish (NFE) AF: 0.186 AC: 12675 AN: 67966

Other (OTH) AF: 0.143 AC: 301 AN: 2112

Alfa AF: 0.166 Hom.: 8677

Bravo AF: 0.147

TwinsUK AF: 0.205 AC: 759

ALSPAC AF: 0.193 AC: 744

ESP6500AA AF: 0.0533 AC: 235

ESP6500EA AF: 0.181 AC: 1556

ExAC AF: 0.174 AC: 21166

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 v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.49
BayesDel_addAF	Benign	-0.73	T
BayesDel_noAF	Benign	-0.68
CADD	Benign	19
DANN	Benign	0.94
DEOGEN2	Benign	0.22	T
Eigen	Benign	-1.1
Eigen_PC	Benign	-0.94
FATHMM_MKL	Uncertain	0.86	D
LIST_S2	Benign	0.78	T
MetaRNN	Benign	0.0017	T
MetaSVM	Benign	-0.95	T
MutationAssessor	Benign	-0.15	N
PhyloP100		1.6
PrimateAI	Uncertain	0.50	T
PROVEAN	Uncertain	-4.1	D
REVEL	Benign	0.088
Sift	Benign	0.44	T
Sift4G	Benign	0.36	T
Polyphen		0.010	B
Vest4		0.22
MutPred		0.44		Loss of glycosylation at S312 (P = 0.0853)
MPC		0.19
ClinPred		0.024	T
GERP RS		2.2
Varity_R		0.27
gMVP		0.27
Mutation Taster		=87/13	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.35		Details are displayed if max score is > 0.2
DS_AL_spliceai		0.35		Position offset: 7

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1895245; hg19: chr5-151772055; COSMIC: COSV54919864; COSMIC: COSV54919864;