chr5-152404655-GCGGAA-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_020167.5(NMUR2):c.454_458del(p.Phe152ArgfsTer97) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000107 in 1,614,138 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Likely benign (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: 𝑓 0.00066 ( 1 hom., cov: 31)
Exomes 𝑓: 0.000049 ( 0 hom. )
Consequence
NMUR2
NM_020167.5 frameshift
NM_020167.5 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 8.99
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]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP6
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Variant 5-152404655-GCGGAA-G is Benign according to our data. Variant chr5-152404655-GCGGAA-G is described in ClinVar as [Likely_benign]. Clinvar id is 764859.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NMUR2 | NM_020167.5 | c.454_458del | p.Phe152ArgfsTer97 | frameshift_variant | 1/4 | ENST00000255262.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NMUR2 | ENST00000255262.4 | c.454_458del | p.Phe152ArgfsTer97 | frameshift_variant | 1/4 | 1 | NM_020167.5 | P1 | |
ENST00000663819.1 | n.183+29446_183+29450del | intron_variant, non_coding_transcript_variant | |||||||
NMUR2 | ENST00000518933.1 | n.273-6516_273-6512del | intron_variant, non_coding_transcript_variant | 3 | |||||
ENST00000663460.1 | n.216+29446_216+29450del | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.000631 AC: 96AN: 152182Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.000171 AC: 43AN: 251158Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135804
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GnomAD4 exome AF: 0.0000493 AC: 72AN: 1461838Hom.: 0 AF XY: 0.0000426 AC XY: 31AN XY: 727220
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GnomAD4 genome ? AF: 0.000657 AC: 100AN: 152300Hom.: 1 Cov.: 31 AF XY: 0.000792 AC XY: 59AN XY: 74464
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 24, 2018 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at