chr5-152404835-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_020167.5(NMUR2):c.279G>A(p.Leu93=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000403 in 1,614,046 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000033 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000041 ( 1 hom. )
Consequence
NMUR2
NM_020167.5 synonymous
NM_020167.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.642
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 Likely_benign. Variant got -5 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.47).
BP6
?
Variant 5-152404835-C-T is Benign according to our data. Variant chr5-152404835-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2655973.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.642 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NMUR2 | NM_020167.5 | c.279G>A | p.Leu93= | synonymous_variant | 1/4 | ENST00000255262.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NMUR2 | ENST00000255262.4 | c.279G>A | p.Leu93= | synonymous_variant | 1/4 | 1 | NM_020167.5 | P1 | |
ENST00000663819.1 | n.183+29622C>T | intron_variant, non_coding_transcript_variant | |||||||
NMUR2 | ENST00000518933.1 | n.273-6691G>A | intron_variant, non_coding_transcript_variant | 3 | |||||
ENST00000663460.1 | n.216+29622C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152040Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.0000557 AC: 14AN: 251408Hom.: 1 AF XY: 0.0000589 AC XY: 8AN XY: 135872
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GnomAD4 exome AF: 0.0000410 AC: 60AN: 1461888Hom.: 1 Cov.: 34 AF XY: 0.0000399 AC XY: 29AN XY: 727242
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GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152158Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74386
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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 | CeGaT Center for Human Genetics Tuebingen | Dec 01, 2022 | NMUR2: BP4, BP7 - |
Computational scores
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BayesDel_noAF
Benign
Cadd
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Dann
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at