rs10515667

Variant names:

• chr5-152401466-G-A
• rs10515667
• NM_020167.5:c.726+2922C>T

Variant summary

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

The NM_020167.5(NMUR2):​c.726+2922C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 152,090 control chromosomes in the GnomAD database, including 2,144 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 0.15 (2144 hom., cov: 32)
• Consequence: NMUR2 NM_020167.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.291
• Publications: 1 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.233 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NMUR2	NM_020167.5	c.726+2922C>T		intron_variant	Intron 1 of 3	ENST00000255262.4	NP_064552.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NMUR2	ENST00000255262.4	c.726+2922C>T		intron_variant	Intron 1 of 3	1	NM_020167.5	ENSP00000255262.4

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22880 AN: 151972 Hom.: 2145 Cov.: 32

Gnomad AFR AF: 0.0613

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.0346

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.149

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.150 AC: 22880 AN: 152090 Hom.: 2144 Cov.: 32 AF XY: 0.151 AC XY: 11260 AN XY: 74356

African (AFR) AF: 0.0614 AC: 2548 AN: 41492

American (AMR) AF: 0.239 AC: 3648 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 535 AN: 3468

East Asian (EAS) AF: 0.0347 AC: 180 AN: 5186

South Asian (SAS) AF: 0.177 AC: 852 AN: 4820

European-Finnish (FIN) AF: 0.183 AC: 1934 AN: 10552

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

European-Non Finnish (NFE) AF: 0.187 AC: 12693 AN: 67988

Other (OTH) AF: 0.147 AC: 310 AN: 2116

Alfa AF: 0.170 Hom.: 347

Bravo AF: 0.153

Asia WGS AF: 0.0860 AC: 300 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.3
DANN	Benign	0.28
PhyloP100		0.29
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: rs10515667; hg19: chr5-151781027;