8-32359709-C-T

Position:

• chr8-32359709-C-T

Variant summary

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

The NM_001159999.3(NRG1):​c.38-236119C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.53 in 151,954 control chromosomes in the GnomAD database, including 21,719 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 0.53 (21719 hom., cov: 33)
• Consequence: NRG1 NM_001159999.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0130

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]

NRG1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.725 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NRG1	NM_001159999.3	c.38-236119C>T		intron_variant			NP_001153471.1
NRG1	NM_001159995.3	c.38-236119C>T		intron_variant			NP_001153467.1
NRG1	NM_001160001.3	c.38-236119C>T		intron_variant			NP_001153473.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NRG1	ENST00000520407.5	c.746-236119C>T		intron_variant		1		ENSP00000434640.1
NRG1	ENST00000523534.5	c.305-236119C>T		intron_variant		5		ENSP00000429067.1
NRG1	ENST00000650866.1	c.38-236119C>T		intron_variant				ENSP00000499045.1

Frequencies

GnomAD3 genomes AF: 0.530 AC: 80431 AN: 151836 Hom.: 21687 Cov.: 33

Gnomad AFR AF: 0.601

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.530 AC: 80515 AN: 151954 Hom.: 21719 Cov.: 33 AF XY: 0.532 AC XY: 39491 AN XY: 74284

Gnomad4 AFR AF: 0.601

Gnomad4 AMR AF: 0.490

Gnomad4 ASJ AF: 0.480

Gnomad4 EAS AF: 0.745

Gnomad4 SAS AF: 0.532

Gnomad4 FIN AF: 0.490

Gnomad4 NFE AF: 0.489

Gnomad4 OTH AF: 0.495

Alfa AF: 0.490 Hom.: 18676

Bravo AF: 0.531

Asia WGS AF: 0.603 AC: 2100 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	11
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1487152; hg19: chr8-32217225;