rs17664708

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_013964.5(NRG1):​c.101-16329C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0998 in 152,096 control chromosomes in the GnomAD database, including 1,112 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 0.10 ( 1112 hom., cov: 31)

Consequence

NRG1
NM_013964.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.413
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.232 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
NRG1NM_013964.5 linkuse as main transcriptc.101-16329C>T intron_variant ENST00000405005.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NRG1ENST00000405005.8 linkuse as main transcriptc.101-16329C>T intron_variant 1 NM_013964.5 A2Q02297-1

Frequencies

GnomAD3 genomes
AF:
0.0998
AC:
15162
AN:
151978
Hom.:
1107
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0267
Gnomad AMI
AF:
0.0901
Gnomad AMR
AF:
0.238
Gnomad ASJ
AF:
0.0649
Gnomad EAS
AF:
0.0475
Gnomad SAS
AF:
0.0526
Gnomad FIN
AF:
0.177
Gnomad MID
AF:
0.0759
Gnomad NFE
AF:
0.111
Gnomad OTH
AF:
0.0980
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0998
AC:
15176
AN:
152096
Hom.:
1112
Cov.:
31
AF XY:
0.104
AC XY:
7760
AN XY:
74340
show subpopulations
Gnomad4 AFR
AF:
0.0266
Gnomad4 AMR
AF:
0.238
Gnomad4 ASJ
AF:
0.0649
Gnomad4 EAS
AF:
0.0474
Gnomad4 SAS
AF:
0.0529
Gnomad4 FIN
AF:
0.177
Gnomad4 NFE
AF:
0.111
Gnomad4 OTH
AF:
0.102
Alfa
AF:
0.111
Hom.:
606
Bravo
AF:
0.106
Asia WGS
AF:
0.0660
AC:
228
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
0.57
DANN
Benign
0.27

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs17664708; hg19: chr8-32437017; API