chr5-152404651-T-C
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP6
The NM_020167.5(NMUR2):c.463A>G(p.Lys155Glu) variant causes a missense change. The variant allele was found at a frequency of 0.000107 in 1,614,066 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.00066 ( 1 hom., cov: 31)
Exomes 𝑓: 0.000049 ( 0 hom. )
Consequence
NMUR2
NM_020167.5 missense
NM_020167.5 missense
Scores
1
10
8
Clinical Significance
Conservation
PhyloP100: 4.73
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 -1 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (MetaRNN=0.16248408).
BP6
?
Variant 5-152404651-T-C is Benign according to our data. Variant chr5-152404651-T-C is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 764858.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=1, Uncertain_significance=1}.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NMUR2 | NM_020167.5 | c.463A>G | p.Lys155Glu | missense_variant | 1/4 | ENST00000255262.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NMUR2 | ENST00000255262.4 | c.463A>G | p.Lys155Glu | missense_variant | 1/4 | 1 | NM_020167.5 | P1 | |
ENST00000663819.1 | n.183+29438T>C | intron_variant, non_coding_transcript_variant | |||||||
NMUR2 | ENST00000518933.1 | n.273-6507A>G | intron_variant, non_coding_transcript_variant | 3 | |||||
ENST00000663460.1 | n.216+29438T>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.000631 AC: 96AN: 152096Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.000171 AC: 43AN: 251196Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135824
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GnomAD4 exome AF: 0.0000493 AC: 72AN: 1461852Hom.: 0 Cov.: 34 AF XY: 0.0000426 AC XY: 31AN XY: 727222
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GnomAD4 genome ? AF: 0.000657 AC: 100AN: 152214Hom.: 1 Cov.: 31 AF XY: 0.000793 AC XY: 59AN XY: 74426
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:1
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 27, 2022 | The c.463A>G (p.K155E) alteration is located in exon 1 (coding exon 1) of the NMUR2 gene. This alteration results from a A to G substitution at nucleotide position 463, causing the lysine (K) at amino acid position 155 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 24, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
Cadd
Uncertain
Dann
Uncertain
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
T
M_CAP
Benign
D
MetaRNN
Benign
T
MetaSVM
Uncertain
T
MutationAssessor
Benign
L
MutationTaster
Benign
D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D
REVEL
Uncertain
Sift
Uncertain
D
Sift4G
Benign
T
Polyphen
D
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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Calibrated prediction
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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