rs982715

Variant names:

• chr5-152391625-A-C
• rs982715
• NM_020167.5:c.*566T>G

Variant summary

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

The NM_020167.5(NMUR2):​c.*566T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 153,034 control chromosomes in the GnomAD database, including 2,092 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 (2079 hom., cov: 32)
  • Exomes 𝑓: 0.16 (13 hom.)
• Consequence: NMUR2 NM_020167.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.504
• Publications: 8 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 (BayesDel_noAF=-0.9).
• 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	c.*566T>G		3_prime_UTR_variant	Exon 4 of 4	ENST00000255262.4	NP_064552.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NMUR2	ENST00000255262.4	c.*566T>G		3_prime_UTR_variant	Exon 4 of 4	1	NM_020167.5	ENSP00000255262.4

Frequencies

GnomAD3 genomes AF: 0.145 AC: 22037 AN: 152124 Hom.: 2082 Cov.: 32

Gnomad AFR AF: 0.0421

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.0344

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.143

GnomAD4 exome AF: 0.159 AC: 126 AN: 792 Hom.: 13 Cov.: 0 AF XY: 0.167 AC XY: 68 AN XY: 406

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AF: 0.203 AC: 24 AN: 118

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 6

South Asian (SAS) AF: 0.139 AC: 5 AN: 36

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.154 AC: 94 AN: 610

Other (OTH) AF: 0.0556 AC: 1 AN: 18

GnomAD4 genome AF: 0.145 AC: 22026 AN: 152242 Hom.: 2079 Cov.: 32 AF XY: 0.145 AC XY: 10815 AN XY: 74412

African (AFR) AF: 0.0421 AC: 1749 AN: 41570

American (AMR) AF: 0.237 AC: 3625 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 535 AN: 3470

East Asian (EAS) AF: 0.0345 AC: 179 AN: 5190

South Asian (SAS) AF: 0.177 AC: 852 AN: 4814

European-Finnish (FIN) AF: 0.182 AC: 1926 AN: 10598

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

European-Non Finnish (NFE) AF: 0.187 AC: 12681 AN: 67994

Other (OTH) AF: 0.141 AC: 299 AN: 2114

Alfa AF: 0.175 Hom.: 3383

Bravo AF: 0.147

Asia WGS AF: 0.0850 AC: 297 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.5
DANN	Benign	0.72
PhyloP100		0.50
Mutation Taster		=100/0	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: rs982715; hg19: chr5-151771186;