chr5-152395580-G-A
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BA1
The NM_020167.5(NMUR2):c.816C>T(p.Val272=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00345 in 1,613,184 control chromosomes in the GnomAD database, including 185 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.018 ( 89 hom., cov: 29)
Exomes 𝑓: 0.0019 ( 96 hom. )
Consequence
NMUR2
NM_020167.5 synonymous
NM_020167.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0760
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 -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.41).
BP6
?
Variant 5-152395580-G-A is Benign according to our data. Variant chr5-152395580-G-A is described in ClinVar as [Benign]. Clinvar id is 780588.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.076 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0621 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NMUR2 | NM_020167.5 | c.816C>T | p.Val272= | synonymous_variant | 3/4 | ENST00000255262.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NMUR2 | ENST00000255262.4 | c.816C>T | p.Val272= | synonymous_variant | 3/4 | 1 | NM_020167.5 | P1 | |
ENST00000663819.1 | n.183+20367G>A | intron_variant, non_coding_transcript_variant | |||||||
NMUR2 | ENST00000518933.1 | n.362C>T | non_coding_transcript_exon_variant | 4/4 | 3 | ||||
ENST00000663460.1 | n.216+20367G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0184 AC: 2787AN: 151766Hom.: 87 Cov.: 29
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GnomAD3 exomes AF: 0.00482 AC: 1208AN: 250760Hom.: 42 AF XY: 0.00334 AC XY: 452AN XY: 135506
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GnomAD4 exome AF: 0.00189 AC: 2768AN: 1461300Hom.: 96 Cov.: 31 AF XY: 0.00160 AC XY: 1163AN XY: 726926
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GnomAD4 genome ? AF: 0.0184 AC: 2793AN: 151884Hom.: 89 Cov.: 29 AF XY: 0.0179 AC XY: 1328AN XY: 74228
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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 | Feb 08, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at