chr6-142062945-G-A

Variant names:

• chr6-142062945-G-A
• rs6907175
• ENST00000604304.1:n.229G>A

Variant summary

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

The ENST00000604304.1(ENSG00000270983):​n.229G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.558 in 1,601,878 control chromosomes in the GnomAD database, including 258,978 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 0.64 (33492 hom., cov: 32)
  • Exomes 𝑓: 0.55 (225486 hom.)
• Consequence: ENSG00000270983 ENST00000604304.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0650

Genes affected

ENSG00000270983 (HGNC:):

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.848 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000270983	ENST00000604304.1	n.229G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
NMBR	ENST00000480652.1	n.268-4482C>T		intron_variant	Intron 2 of 2	5

Frequencies

GnomAD3 genomes AF: 0.644 AC: 97857 AN: 151878 Hom.: 33430 Cov.: 32

Gnomad AFR AF: 0.853

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.703

Gnomad ASJ AF: 0.367

Gnomad EAS AF: 0.869

Gnomad SAS AF: 0.565

Gnomad FIN AF: 0.585

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.643

GnomAD4 exome AF: 0.549 AC: 796110 AN: 1449884 Hom.: 225486 Cov.: 33 AF XY: 0.546 AC XY: 393675 AN XY: 721524

Gnomad4 AFR exome AF: 0.865

Gnomad4 AMR exome AF: 0.779

Gnomad4 ASJ exome AF: 0.387

Gnomad4 EAS exome AF: 0.887

Gnomad4 SAS exome AF: 0.540

Gnomad4 FIN exome AF: 0.579

Gnomad4 NFE exome AF: 0.521

Gnomad4 OTH exome AF: 0.566

GnomAD4 genome AF: 0.645 AC: 97981 AN: 151994 Hom.: 33492 Cov.: 32 AF XY: 0.650 AC XY: 48291 AN XY: 74284

Gnomad4 AFR AF: 0.854

Gnomad4 AMR AF: 0.703

Gnomad4 ASJ AF: 0.367

Gnomad4 EAS AF: 0.869

Gnomad4 SAS AF: 0.565

Gnomad4 FIN AF: 0.585

Gnomad4 NFE AF: 0.519

Gnomad4 OTH AF: 0.644

Alfa AF: 0.590 Hom.: 3489

Bravo AF: 0.668

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.8
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6907175; hg19: chr6-142384082;