10-82725902-A-C

Position:

• chr10-82725902-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001010848.4(NRG3):​c.954-12675A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.871 in 152,116 control chromosomes in the GnomAD database, including 57,870 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 0.87 (57870 hom., cov: 32)
• Consequence: NRG3 NM_001010848.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.802

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.91 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NRG3	NM_001010848.4	c.954-12675A>C		intron_variant		ENST00000372141.7	NP_001010848.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NRG3	ENST00000372141.7	c.954-12675A>C		intron_variant		1	NM_001010848.4	ENSP00000361214	A2

Frequencies

GnomAD3 genomes AF: 0.871 AC: 132388 AN: 151996 Hom.: 57805 Cov.: 32

Gnomad AFR AF: 0.917

Gnomad AMI AF: 0.780

Gnomad AMR AF: 0.889

Gnomad ASJ AF: 0.857

Gnomad EAS AF: 0.883

Gnomad SAS AF: 0.825

Gnomad FIN AF: 0.867

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.844

Gnomad OTH AF: 0.877

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

GnomAD4 genome AF: 0.871 AC: 132514 AN: 152116 Hom.: 57870 Cov.: 32 AF XY: 0.871 AC XY: 64722 AN XY: 74338

Gnomad4 AFR AF: 0.917

Gnomad4 AMR AF: 0.889

Gnomad4 ASJ AF: 0.857

Gnomad4 EAS AF: 0.884

Gnomad4 SAS AF: 0.824

Gnomad4 FIN AF: 0.867

Gnomad4 NFE AF: 0.844

Gnomad4 OTH AF: 0.878

Alfa AF: 0.838 Hom.: 20351

Bravo AF: 0.878

Asia WGS AF: 0.869 AC: 3021 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.43
DANN	Benign	0.38

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

Other links and lift over

dbSNP: rs2820096; hg19: chr10-84485658;