rs7830691
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001159999.3(NRG1):c.38-266264C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00233 in 151,970 control chromosomes in the GnomAD database, including 1 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 0.0023 ( 1 hom., cov: 31)
Consequence
NRG1
NM_001159999.3 intron
NM_001159999.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.375
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BS2
High AC in GnomAd4 at 354 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NRG1 | NM_001159999.3 | c.38-266264C>G | intron_variant | NP_001153471.1 | ||||
NRG1 | NM_001159995.3 | c.38-266264C>G | intron_variant | NP_001153467.1 | ||||
NRG1 | NM_001160001.3 | c.38-266264C>G | intron_variant | NP_001153473.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NRG1 | ENST00000520407.5 | c.746-266264C>G | intron_variant | 1 | ENSP00000434640.1 | |||||
NRG1 | ENST00000523534.5 | c.305-266264C>G | intron_variant | 5 | ENSP00000429067.1 | |||||
NRG1 | ENST00000650866.1 | c.38-266264C>G | intron_variant | ENSP00000499045.1 |
Frequencies
GnomAD3 genomes AF: 0.00232 AC: 353AN: 151850Hom.: 1 Cov.: 31
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31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.00233 AC: 354AN: 151970Hom.: 1 Cov.: 31 AF XY: 0.00217 AC XY: 161AN XY: 74278
GnomAD4 genome
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at