rs10515665

Positions:

• chr5-152400623-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020167.5(NMUR2):​c.727-2479A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 152,152 control chromosomes in the GnomAD database, including 2,089 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 (2089 hom., cov: 32)
• Consequence: NMUR2 NM_020167.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.441

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• 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/exons	MANE	UniProt
NMUR2	NM_020167.5	c.727-2479A>T		intron_variant		ENST00000255262.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NMUR2	ENST00000255262.4	c.727-2479A>T		intron_variant		1	NM_020167.5	P1
	ENST00000663819.1	n.183+25410T>A		intron_variant, non_coding_transcript_variant
NMUR2	ENST00000518933.1	n.273-2479A>T		intron_variant, non_coding_transcript_variant		3
	ENST00000663460.1	n.216+25410T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22256 AN: 152034 Hom.: 2092 Cov.: 32

Gnomad AFR AF: 0.0479

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.0344

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.169

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.146 AC: 22246 AN: 152152 Hom.: 2089 Cov.: 32 AF XY: 0.147 AC XY: 10922 AN XY: 74396

Gnomad4 AFR AF: 0.0478

Gnomad4 AMR AF: 0.238

Gnomad4 ASJ AF: 0.154

Gnomad4 EAS AF: 0.0345

Gnomad4 SAS AF: 0.177

Gnomad4 FIN AF: 0.181

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.142

Alfa AF: 0.171 Hom.: 341

Bravo AF: 0.149

Asia WGS AF: 0.0840 AC: 294 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.48
DANN	Benign	0.46

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

Publications

LitVar

Other links and lift over

dbSNP: rs10515665; hg19: chr5-151780184;