chr8-31641892-C-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000520407.5(NRG1):c.745+1163C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 151,828 control chromosomes in the GnomAD database, including 4,737 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 0.24 ( 4737 hom., cov: 32)
Exomes 𝑓: 0.17 ( 0 hom. )
Consequence
NRG1
ENST00000520407.5 intron
ENST00000520407.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.43
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.55).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NRG1 | NM_001159995.3 | c.37+2461C>T | intron_variant | ||||
NRG1 | NM_001159999.3 | c.37+2461C>T | intron_variant | ||||
NRG1 | NM_001160001.3 | c.37+2461C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NRG1 | ENST00000520407.5 | c.745+1163C>T | intron_variant | 1 | |||||
NRG1 | ENST00000519301.6 | c.37+2461C>T | intron_variant | 5 | |||||
NRG1 | ENST00000523534.5 | c.304+1163C>T | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.238 AC: 36125AN: 151704Hom.: 4736 Cov.: 32
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GnomAD4 exome AF: 0.167 AC: 1AN: 6Hom.: 0 AF XY: 0.250 AC XY: 1AN XY: 4
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GnomAD4 genome ? AF: 0.238 AC: 36145AN: 151822Hom.: 4737 Cov.: 32 AF XY: 0.230 AC XY: 17069AN XY: 74180
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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