chr5-152404887-A-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_020167.5(NMUR2):c.227T>G(p.Met76Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000975 in 1,614,094 control chromosomes in the GnomAD database, including 5 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00072 ( 2 hom., cov: 31)
Exomes 𝑓: 0.0010 ( 3 hom. )
Consequence
NMUR2
NM_020167.5 missense
NM_020167.5 missense
Scores
9
5
5
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 Likely_benign. Variant got -4 ACMG points.
BS2
?
High Homozygotes in GnomAd at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NMUR2 | NM_020167.5 | c.227T>G | p.Met76Arg | missense_variant | 1/4 | ENST00000255262.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NMUR2 | ENST00000255262.4 | c.227T>G | p.Met76Arg | missense_variant | 1/4 | 1 | NM_020167.5 | P1 | |
ENST00000663819.1 | n.183+29674A>C | intron_variant, non_coding_transcript_variant | |||||||
NMUR2 | ENST00000518933.1 | n.273-6743T>G | intron_variant, non_coding_transcript_variant | 3 | |||||
ENST00000663460.1 | n.216+29674A>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.000717 AC: 109AN: 152086Hom.: 2 Cov.: 31
GnomAD3 genomes
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GnomAD3 exomes AF: 0.000589 AC: 148AN: 251462Hom.: 0 AF XY: 0.000640 AC XY: 87AN XY: 135902
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GnomAD4 exome AF: 0.00100 AC: 1465AN: 1461890Hom.: 3 Cov.: 34 AF XY: 0.000939 AC XY: 683AN XY: 727244
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GnomAD4 genome ? AF: 0.000716 AC: 109AN: 152204Hom.: 2 Cov.: 31 AF XY: 0.000511 AC XY: 38AN XY: 74426
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 15, 2021 | The c.227T>G (p.M76R) alteration is located in exon 1 (coding exon 1) of the NMUR2 gene. This alteration results from a T to G substitution at nucleotide position 227, causing the methionine (M) at amino acid position 76 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Pathogenic
Cadd
Uncertain
Dann
Uncertain
DEOGEN2
Benign
T
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D
M_CAP
Benign
T
MetaRNN
Uncertain
D
MetaSVM
Benign
T
MutationAssessor
Pathogenic
M
MutationTaster
Benign
D
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D
REVEL
Pathogenic
Sift
Pathogenic
D
Sift4G
Pathogenic
D
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