rs225604
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002511.4(NMBR):c.-664+15615C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.406 in 151,972 control chromosomes in the GnomAD database, including 13,091 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 0.41 ( 13091 hom., cov: 32)
Consequence
NMBR
NM_002511.4 intron
NM_002511.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.509
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NMBR | NM_002511.4 | c.-664+15615C>T | intron_variant | ENST00000258042.2 | |||
NMBR | NM_001324307.2 | c.-23+11127C>T | intron_variant | ||||
NMBR | NM_001324308.2 | c.-23+15615C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NMBR | ENST00000258042.2 | c.-664+15615C>T | intron_variant | 1 | NM_002511.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.406 AC: 61685AN: 151854Hom.: 13083 Cov.: 32
GnomAD3 genomes
?
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61685
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.406 AC: 61721AN: 151972Hom.: 13091 Cov.: 32 AF XY: 0.400 AC XY: 29738AN XY: 74256
GnomAD4 genome
?
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61721
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32
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29738
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74256
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1273
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at