5-139848102-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_004883.3(NRG2):c.2368G>A(p.Ala790Thr) variant causes a missense change. The variant allele was found at a frequency of 0.000127 in 1,478,526 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000046 ( 0 hom., cov: 29)
Exomes 𝑓: 0.00014 ( 0 hom. )
Consequence
NRG2
NM_004883.3 missense
NM_004883.3 missense
Scores
2
6
9
Clinical Significance
Conservation
PhyloP100: 4.32
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 Uncertain_significance. Variant got 1 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (MetaRNN=0.36685267).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NRG2 | NM_004883.3 | c.2368G>A | p.Ala790Thr | missense_variant | 10/10 | ENST00000361474.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NRG2 | ENST00000361474.6 | c.2368G>A | p.Ala790Thr | missense_variant | 10/10 | 1 | NM_004883.3 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000461 AC: 7AN: 151720Hom.: 0 Cov.: 29
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GnomAD3 exomes AF: 0.0000375 AC: 3AN: 79990Hom.: 0 AF XY: 0.0000218 AC XY: 1AN XY: 45902
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GnomAD4 exome AF: 0.000136 AC: 181AN: 1326806Hom.: 0 Cov.: 33 AF XY: 0.000127 AC XY: 83AN XY: 654146
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GnomAD4 genome ? AF: 0.0000461 AC: 7AN: 151720Hom.: 0 Cov.: 29 AF XY: 0.0000405 AC XY: 3AN XY: 74102
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 19, 2023 | The c.2392G>A (p.A798T) alteration is located in exon 11 (coding exon 11) of the NRG2 gene. This alteration results from a G to A substitution at nucleotide position 2392, causing the alanine (A) at amino acid position 798 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Pathogenic
Dann
Uncertain
Eigen
Uncertain
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;D;D;D;D
M_CAP
Pathogenic
D
MetaRNN
Benign
T;T;T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D;D;D;D;D;D
PrimateAI
Pathogenic
D
PROVEAN
Benign
N;N;N;N;N;N
REVEL
Benign
Sift
Uncertain
D;D;D;D;D;D
Sift4G
Uncertain
D;D;D;D;T;D
Polyphen
1.0, 1.0, 1.0
.;D;D;.;D;D
Vest4
MVP
MPC
1.8
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at