ENST00000604304.1:n.229G>A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000604304.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000270983	ENST00000604304.1	TSL:6	n.229G>A		non_coding_transcript_exon	Exon 1 of 1
	NMBR	ENST00000480652.1	TSL:5	n.268-4482C>T		intron	N/A

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

African (AFR) AF: 0.865 AC: 28440 AN: 32882

American (AMR) AF: 0.779 AC: 34319 AN: 44062

Ashkenazi Jewish (ASJ) AF: 0.387 AC: 10089 AN: 26044

East Asian (EAS) AF: 0.887 AC: 34644 AN: 39036

South Asian (SAS) AF: 0.540 AC: 46140 AN: 85418

European-Finnish (FIN) AF: 0.579 AC: 30613 AN: 52866

Middle Eastern (MID) AF: 0.461 AC: 2625 AN: 5700

European-Non Finnish (NFE) AF: 0.521 AC: 575312 AN: 1103962

Other (OTH) AF: 0.566 AC: 33928 AN: 59914

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

African (AFR) AF: 0.854 AC: 35409 AN: 41484

American (AMR) AF: 0.703 AC: 10712 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.367 AC: 1272 AN: 3466

East Asian (EAS) AF: 0.869 AC: 4489 AN: 5166

South Asian (SAS) AF: 0.565 AC: 2720 AN: 4816

European-Finnish (FIN) AF: 0.585 AC: 6185 AN: 10564

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.519 AC: 35245 AN: 67950

Other (OTH) AF: 0.644 AC: 1358 AN: 2110

Alfa AF: 0.590 Hom.: 3489

Bravo AF: 0.668

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.8
DANN	Benign	0.54
PhyloP100		0.065

Splicing

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

Other links and lift over

dbSNP: rs6907175; hg19: chr6-142384082;