5-152392494-G-T

Variant summary

Our verdict is Benign. Variant got -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. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.

Frequency

Genomes: 𝑓 0.14 ( 2087 hom., cov: 32)
Exomes 𝑓: 0.18 ( 26478 hom. )

Consequence

NMUR2
NM_020167.5 missense

Scores

4
14

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.55
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

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
NMUR2NM_020167.5 linkc.945C>A p.Phe315Leu 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
NMUR2ENST00000255262.4 linkc.945C>A p.Phe315Leu missense_variant Exon 4 of 4 1 NM_020167.5 ENSP00000255262.4 Q9GZQ4
ENSG00000286749ENST00000663460.1 linkn.216+17281G>T intron_variant Intron 1 of 3
ENSG00000286749ENST00000663819.1 linkn.183+17281G>T intron_variant Intron 1 of 3

Frequencies

GnomAD3 genomes
AF:
0.145
AC:
22042
AN:
152046
Hom.:
2090
Cov.:
32
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:
0.0345
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
GnomAD3 exomes
AF:
0.184
AC:
45861
AN:
249682
Hom.:
5328
AF XY:
0.182
AC XY:
24570
AN XY:
134902
show subpopulations
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 SAS exome
AF:
0.191
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
show subpopulations
Gnomad4 AFR exome
AF:
0.0382
Gnomad4 AMR exome
AF:
0.340
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:
22031
AN:
152164
Hom.:
2087
Cov.:
32
AF XY:
0.145
AC XY:
10821
AN XY:
74402
show subpopulations
Gnomad4 AFR
AF:
0.0423
Gnomad4 AMR
AF:
0.237
Gnomad4 ASJ
AF:
0.154
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:
0.169
Hom.:
5802
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 v4.3

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
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

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

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