chr4-55601047-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_006681.4(NMU):​c.436-472T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 152,078 control chromosomes in the GnomAD database, including 2,434 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.17 ( 2434 hom., cov: 32)

Consequence

NMU
NM_006681.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.753
Variant links:
Genes affected
NMU (HGNC:7859): (neuromedin U) This gene encodes a member of the neuromedin family of neuropeptides. The encoded protein is a precursor that is proteolytically processed to generate a biologically active neuropeptide that plays a role in pain, stress, immune-mediated inflammatory diseases and feeding regulation. Increased expression of this gene was observed in renal, pancreatic and lung cancers. Alternative splicing results in multiple transcript variants encoding different isoforms. Some of these isoforms may undergo similar processing to generate the mature peptide. [provided by RefSeq, Jul 2015]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
NMUNM_006681.4 linkuse as main transcriptc.436-472T>C intron_variant ENST00000264218.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NMUENST00000264218.7 linkuse as main transcriptc.436-472T>C intron_variant 1 NM_006681.4 P1

Frequencies

GnomAD3 genomes
AF:
0.174
AC:
26379
AN:
151962
Hom.:
2430
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.134
Gnomad AMI
AF:
0.196
Gnomad AMR
AF:
0.165
Gnomad ASJ
AF:
0.153
Gnomad EAS
AF:
0.0924
Gnomad SAS
AF:
0.241
Gnomad FIN
AF:
0.253
Gnomad MID
AF:
0.142
Gnomad NFE
AF:
0.190
Gnomad OTH
AF:
0.160
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.174
AC:
26398
AN:
152078
Hom.:
2434
Cov.:
32
AF XY:
0.176
AC XY:
13067
AN XY:
74336
show subpopulations
Gnomad4 AFR
AF:
0.134
Gnomad4 AMR
AF:
0.165
Gnomad4 ASJ
AF:
0.153
Gnomad4 EAS
AF:
0.0923
Gnomad4 SAS
AF:
0.242
Gnomad4 FIN
AF:
0.253
Gnomad4 NFE
AF:
0.190
Gnomad4 OTH
AF:
0.163
Alfa
AF:
0.188
Hom.:
996
Bravo
AF:
0.160
Asia WGS
AF:
0.198
AC:
680
AN:
3446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
0.69
DANN
Benign
0.47

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: rs13434995; hg19: chr4-56467214; API