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GeneBe

5-152392467-G-T

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_020167.5(NMUR2):c.972C>A(p.Pro324=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0107 in 1,613,818 control chromosomes in the GnomAD database, including 120 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0075 ( 8 hom., cov: 32)
Exomes 𝑓: 0.011 ( 112 hom. )

Consequence

NMUR2
NM_020167.5 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.40
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.48).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 5-152392467-G-T is Benign according to our data. Variant chr5-152392467-G-T is described in ClinVar as [Benign]. Clinvar id is 777808.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=1.4 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 8 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
NMUR2NM_020167.5 linkuse as main transcriptc.972C>A p.Pro324= synonymous_variant 4/4 ENST00000255262.4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NMUR2ENST00000255262.4 linkuse as main transcriptc.972C>A p.Pro324= synonymous_variant 4/41 NM_020167.5 P1
ENST00000663819.1 linkuse as main transcriptn.183+17254G>T intron_variant, non_coding_transcript_variant
ENST00000663460.1 linkuse as main transcriptn.216+17254G>T intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00750
AC:
1142
AN:
152172
Hom.:
8
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00200
Gnomad AMI
AF:
0.0352
Gnomad AMR
AF:
0.00452
Gnomad ASJ
AF:
0.0124
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00735
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.0121
Gnomad OTH
AF:
0.00526
GnomAD3 exomes
AF:
0.00816
AC:
2049
AN:
251036
Hom.:
18
AF XY:
0.00823
AC XY:
1117
AN XY:
135664
show subpopulations
Gnomad AFR exome
AF:
0.00179
Gnomad AMR exome
AF:
0.00292
Gnomad ASJ exome
AF:
0.0131
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000294
Gnomad FIN exome
AF:
0.00787
Gnomad NFE exome
AF:
0.0136
Gnomad OTH exome
AF:
0.0106
GnomAD4 exome
AF:
0.0110
AC:
16137
AN:
1461528
Hom.:
112
Cov.:
35
AF XY:
0.0107
AC XY:
7782
AN XY:
727058
show subpopulations
Gnomad4 AFR exome
AF:
0.00161
Gnomad4 AMR exome
AF:
0.00322
Gnomad4 ASJ exome
AF:
0.0126
Gnomad4 EAS exome
AF:
0.0000504
Gnomad4 SAS exome
AF:
0.000499
Gnomad4 FIN exome
AF:
0.00811
Gnomad4 NFE exome
AF:
0.0130
Gnomad4 OTH exome
AF:
0.0106
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00751
AC:
1143
AN:
152290
Hom.:
8
Cov.:
32
AF XY:
0.00731
AC XY:
544
AN XY:
74460
show subpopulations
Gnomad4 AFR
AF:
0.00200
Gnomad4 AMR
AF:
0.00451
Gnomad4 ASJ
AF:
0.0124
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00735
Gnomad4 NFE
AF:
0.0121
Gnomad4 OTH
AF:
0.00520
Alfa
AF:
0.0110
Hom.:
6
Bravo
AF:
0.00727
Asia WGS
AF:
0.000866
AC:
3
AN:
3478
EpiCase
AF:
0.0107
EpiControl
AF:
0.0117

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 submitterclinical testingInvitaeDec 31, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.48
Cadd
Benign
7.0
Dann
Benign
0.69

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs35771607; hg19: chr5-151772028; API