chr5-152395471-G-A
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Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_020167.5(NMUR2):c.925C>T(p.His309Tyr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000372 in 1,613,360 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000020 ( 0 hom., cov: 30)
Exomes 𝑓: 0.0000021 ( 0 hom. )
Consequence
NMUR2
NM_020167.5 missense
NM_020167.5 missense
Scores
7
7
5
Clinical Significance
Conservation
PhyloP100: 8.72
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 Uncertain_significance. Variant got 4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.845
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NMUR2 | NM_020167.5 | c.925C>T | p.His309Tyr | missense_variant | 3/4 | ENST00000255262.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NMUR2 | ENST00000255262.4 | c.925C>T | p.His309Tyr | missense_variant | 3/4 | 1 | NM_020167.5 | P1 | |
ENST00000663819.1 | n.183+20258G>A | intron_variant, non_coding_transcript_variant | |||||||
ENST00000663460.1 | n.216+20258G>A | intron_variant, non_coding_transcript_variant | |||||||
NMUR2 | ENST00000518933.1 | downstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 151988Hom.: 0 Cov.: 30
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GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461372Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 726996
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GnomAD4 genome AF: 0.0000197 AC: 3AN: 151988Hom.: 0 Cov.: 30 AF XY: 0.0000269 AC XY: 2AN XY: 74232
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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 26, 2021 | The c.925C>T (p.H309Y) alteration is located in exon 3 (coding exon 3) of the NMUR2 gene. This alteration results from a C to T substitution at nucleotide position 925, causing the histidine (H) at amino acid position 309 to be replaced by a tyrosine (Y). 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
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D
M_CAP
Benign
D
MetaRNN
Pathogenic
D
MetaSVM
Uncertain
T
MutationAssessor
Benign
L
MutationTaster
Benign
D
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D
REVEL
Uncertain
Sift
Uncertain
D
Sift4G
Benign
T
Polyphen
D
Vest4
MutPred
Loss of catalytic residue at H309 (P = 0.0683);
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
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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