rs10094655

chr8-32536630-T-Achr8-32536630-T-G

Variant summary

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

The ENST00000520407.5(NRG1):c.746-59198T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 151,870 control chromosomes in the GnomAD database, including 2,335 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 0.11 (2335 hom., cov: 32)
• Consequence: NRG1 ENST00000520407.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.612

Genes affected

NRG1 (HGNC:7997): (neuregulin 1) The protein encoded by this gene is a membrane glycoprotein that mediates cell-cell signaling and plays a critical role in the growth and development of multiple organ systems. An extraordinary variety of different isoforms are produced from this gene through alternative promoter usage and splicing. These isoforms are expressed in a tissue-specific manner and differ significantly in their structure, and are classified as types I, II, III, IV, V and VI. Dysregulation of this gene has been linked to diseases such as cancer, schizophrenia, and bipolar disorder (BPD). [provided by RefSeq, Apr 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.572 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NRG1	NM_001159995.3	c.38-59198T>A		intron_variant
NRG1	NM_001159999.3	c.38-59198T>A		intron_variant
NRG1	NM_001160001.3	c.38-59198T>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NRG1	ENST00000520407.5	c.746-59198T>A		intron_variant		1
NRG1	ENST00000519301.6	c.38-59198T>A		intron_variant		5
NRG1	ENST00000523534.5	c.305-59198T>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16701 AN: 151752 Hom.: 2323 Cov.: 32

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0887

Gnomad ASJ AF: 0.0245

Gnomad EAS AF: 0.588

Gnomad SAS AF: 0.0986

Gnomad FIN AF: 0.0173

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0187

Gnomad OTH AF: 0.0932

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

GnomAD4 genome AF: 0.110 AC: 16739 AN: 151870 Hom.: 2335 Cov.: 32 AF XY: 0.112 AC XY: 8320 AN XY: 74246

Gnomad4 AFR AF: 0.245

Gnomad4 AMR AF: 0.0890

Gnomad4 ASJ AF: 0.0245

Gnomad4 EAS AF: 0.589

Gnomad4 SAS AF: 0.0980

Gnomad4 FIN AF: 0.0173

Gnomad4 NFE AF: 0.0187

Gnomad4 OTH AF: 0.0908

Alfa AF: 0.0645 Hom.: 115

Bravo AF: 0.126

Asia WGS AF: 0.256 AC: 891 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
Cadd	Benign	7.1
Dann	Benign	0.93

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10094655; hg19: chr8-32394147;