rs1923563

Variant names:

• chr10-82923169-C-T
• rs1923563
• NM_001010848.4:c.1055-28300C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001010848.4(NRG3):​c.1055-28300C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.378 in 152,070 control chromosomes in the GnomAD database, including 11,358 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 0.38 (11358 hom., cov: 32)
• Consequence: NRG3 NM_001010848.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0180
• Publications: 0 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.614 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NRG3	NM_001010848.4	c.1055-28300C>T		intron_variant	Intron 4 of 8	ENST00000372141.7	NP_001010848.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NRG3	ENST00000372141.7	c.1055-28300C>T		intron_variant	Intron 4 of 8	1	NM_001010848.4	ENSP00000361214.2

Frequencies

GnomAD3 genomes AF: 0.379 AC: 57516 AN: 151952 Hom.: 11350 Cov.: 32

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.633

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.356

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.378 AC: 57557 AN: 152070 Hom.: 11358 Cov.: 32 AF XY: 0.390 AC XY: 28952 AN XY: 74326

African (AFR) AF: 0.437 AC: 18126 AN: 41496

American (AMR) AF: 0.408 AC: 6229 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.336 AC: 1165 AN: 3470

East Asian (EAS) AF: 0.632 AC: 3260 AN: 5158

South Asian (SAS) AF: 0.473 AC: 2278 AN: 4814

European-Finnish (FIN) AF: 0.439 AC: 4632 AN: 10546

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.305 AC: 20746 AN: 67992

Other (OTH) AF: 0.354 AC: 746 AN: 2110

Alfa AF: 0.348 Hom.: 1186

Bravo AF: 0.378

Asia WGS AF: 0.524 AC: 1821 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.30
PhyloP100		0.018
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1923563; hg19: chr10-84682925;