NM_002511.4:c.*1065C>T

Variant names:

• chr6-142074583-G-A
• rs2717
• NM_002511.4:c.*1065C>T

Variant summary

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

The NM_002511.4(NMBR):​c.*1065C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.62 in 151,970 control chromosomes in the GnomAD database, including 30,550 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 0.62 (30550 hom., cov: 32)
• Consequence: NMBR NM_002511.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.648
• Publications: 10 publications found

Genes affected

NMBR (HGNC:7843): (neuromedin B receptor) This gene encodes a 7-transmembrane G protein-coupled receptor that binds neuromedin B, which is a growth factor and mitogen for gastrointestinal epithelial tissue and for normal and neoplastic lung. This receptor may play a role in smooth muscle contraction, neuronal responses, and the regulation of cell growth. Antagonists of this receptor have a potential therapeutic use in inhibiting tumor cell growth. Polymorphisms in this gene may be associated with a susceptibility for schizophrenia. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Apr 2016]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.823 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NMBR	NM_002511.4	c.*1065C>T		3_prime_UTR_variant	Exon 4 of 4	ENST00000258042.2	NP_002502.2
NMBR	NM_001324307.2	c.*1065C>T		3_prime_UTR_variant	Exon 4 of 4		NP_001311236.1
NMBR	NM_001324308.2	c.*1065C>T		3_prime_UTR_variant	Exon 3 of 3		NP_001311237.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NMBR	ENST00000258042.2	c.*1065C>T		3_prime_UTR_variant	Exon 4 of 4	1	NM_002511.4	ENSP00000258042.1
NMBR	ENST00000480652.1	n.180-299C>T		intron_variant	Intron 1 of 2	5

Frequencies

GnomAD3 genomes AF: 0.619 AC: 94056 AN: 151854 Hom.: 30515 Cov.: 32

Gnomad AFR AF: 0.788

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.689

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.844

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.585

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.617

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

GnomAD4 genome AF: 0.620 AC: 94148 AN: 151970 Hom.: 30550 Cov.: 32 AF XY: 0.625 AC XY: 46388 AN XY: 74278

African (AFR) AF: 0.788 AC: 32719 AN: 41506

American (AMR) AF: 0.689 AC: 10525 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.366 AC: 1271 AN: 3470

East Asian (EAS) AF: 0.844 AC: 4367 AN: 5176

South Asian (SAS) AF: 0.497 AC: 2393 AN: 4814

European-Finnish (FIN) AF: 0.585 AC: 6157 AN: 10526

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.513 AC: 34840 AN: 67900

Other (OTH) AF: 0.613 AC: 1294 AN: 2112

Alfa AF: 0.551 Hom.: 65007

Bravo AF: 0.642

Asia WGS AF: 0.654 AC: 2269 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.7
DANN	Benign	0.61
PhyloP100		0.65

Splicing

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

Other links and lift over

dbSNP: rs2717; hg19: chr6-142395720;