NM_001010848.4:c.1028-9145G>C
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001010848.4(NRG3):c.1028-9145G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.454 in 151,860 control chromosomes in the GnomAD database, including 15,997 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 0.45 ( 15997 hom., cov: 31)
Consequence
NRG3
NM_001010848.4 intron
NM_001010848.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.236
Publications
2 publications found
Genes affected
NRG3 (HGNC:7999): (neuregulin 3) This gene is a member of the neuregulin gene family. This gene family encodes ligands for the transmembrane tyrosine kinase receptors ERBB3 and ERBB4 - members of the epidermal growth factor receptor family. Ligand binding activates intracellular signaling cascades and the induction of cellular responses including proliferation, migration, differentiation, and survival or apoptosis. This gene encodes neuregulin 3 (NRG3). NRG3 has been shown to activate the tyrosine phosphorylation of its cognate receptor, ERBB4, and is thought to influence neuroblast proliferation, migration and differentiation by signalling through ERBB4. NRG3 also promotes mammary differentiation during embryogenesis. Linkage studies have implicated this gene as a susceptibility locus for schizophrenia and schizoaffective disorder. Alternative splicing results in multiple transcript variants encoding distinct isoforms. Additional transcript variants have been described but their biological validity has not been verified.[provided by RefSeq, Sep 2009]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.484 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.454 AC: 68953AN: 151740Hom.: 15988 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
68953
AN:
151740
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.454 AC: 68990AN: 151860Hom.: 15997 Cov.: 31 AF XY: 0.448 AC XY: 33242AN XY: 74224 show subpopulations
GnomAD4 genome
AF:
AC:
68990
AN:
151860
Hom.:
Cov.:
31
AF XY:
AC XY:
33242
AN XY:
74224
show subpopulations
African (AFR)
AF:
AC:
19863
AN:
41388
American (AMR)
AF:
AC:
5808
AN:
15260
Ashkenazi Jewish (ASJ)
AF:
AC:
1715
AN:
3466
East Asian (EAS)
AF:
AC:
643
AN:
5152
South Asian (SAS)
AF:
AC:
2189
AN:
4796
European-Finnish (FIN)
AF:
AC:
4360
AN:
10548
Middle Eastern (MID)
AF:
AC:
120
AN:
294
European-Non Finnish (NFE)
AF:
AC:
33159
AN:
67932
Other (OTH)
AF:
AC:
930
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1874
3747
5621
7494
9368
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
636
1272
1908
2544
3180
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1043
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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