rs889022
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004883.3(NRG2):c.991+13A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 1,609,466 control chromosomes in the GnomAD database, including 35,128 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 0.25 ( 5792 hom., cov: 32)
Exomes 𝑓: 0.19 ( 29336 hom. )
Consequence
NRG2
NM_004883.3 intron
NM_004883.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.189
Genes affected
NRG2 (HGNC:7998): (neuregulin 2) This gene encodes a novel member of the neuregulin family of growth and differentiation factors. Through interaction with the ERBB family of receptors, this protein induces the growth and differentiation of epithelial, neuronal, glial, and other types of cells. The gene consists of 12 exons and the genomic structure is similar to that of neuregulin 1, another member of the neuregulin family of ligands. The products of these genes mediate distinct biological processes by acting at different sites in tissues and eliciting different biological responses in cells. This gene is located close to the region for demyelinating Charcot-Marie-Tooth disease locus, but is not responsible for this disease. Alternative transcript variants encoding distinct isoforms have been described. [provided by RefSeq, May 2010]
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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=-0.86).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NRG2 | NM_004883.3 | c.991+13A>G | intron_variant | ENST00000361474.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NRG2 | ENST00000361474.6 | c.991+13A>G | intron_variant | 1 | NM_004883.3 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.247 AC: 37613AN: 152056Hom.: 5754 Cov.: 32
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GnomAD3 exomes AF: 0.195 AC: 48566AN: 249432Hom.: 5690 AF XY: 0.197 AC XY: 26515AN XY: 134846
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GnomAD4 exome AF: 0.191 AC: 278928AN: 1457292Hom.: 29336 Cov.: 30 AF XY: 0.193 AC XY: 140277AN XY: 725250
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GnomAD4 genome ? AF: 0.248 AC: 37710AN: 152174Hom.: 5792 Cov.: 32 AF XY: 0.243 AC XY: 18049AN XY: 74398
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at