chr5-152392467-G-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_020167.5(NMUR2):c.972C>A(p.Pro324=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0107 in 1,613,818 control chromosomes in the GnomAD database, including 120 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0075 ( 8 hom., cov: 32)
Exomes 𝑓: 0.011 ( 112 hom. )
Consequence
NMUR2
NM_020167.5 synonymous
NM_020167.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.40
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 Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.48).
BP6
?
Variant 5-152392467-G-T is Benign according to our data. Variant chr5-152392467-G-T is described in ClinVar as [Benign]. Clinvar id is 777808.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=1.4 with no splicing effect.
BS2
?
High Homozygotes in GnomAd at 8 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NMUR2 | NM_020167.5 | c.972C>A | p.Pro324= | synonymous_variant | 4/4 | ENST00000255262.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NMUR2 | ENST00000255262.4 | c.972C>A | p.Pro324= | synonymous_variant | 4/4 | 1 | NM_020167.5 | P1 | |
ENST00000663819.1 | n.183+17254G>T | intron_variant, non_coding_transcript_variant | |||||||
ENST00000663460.1 | n.216+17254G>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.00750 AC: 1142AN: 152172Hom.: 8 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.00816 AC: 2049AN: 251036Hom.: 18 AF XY: 0.00823 AC XY: 1117AN XY: 135664
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GnomAD4 exome AF: 0.0110 AC: 16137AN: 1461528Hom.: 112 Cov.: 35 AF XY: 0.0107 AC XY: 7782AN XY: 727058
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GnomAD4 genome ? AF: 0.00751 AC: 1143AN: 152290Hom.: 8 Cov.: 32 AF XY: 0.00731 AC XY: 544AN XY: 74460
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at