chr8-31640457-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The ENST00000520407.5(NRG1):c.473C>T(p.Ala158Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00345 in 1,566,488 control chromosomes in the GnomAD database, including 164 homozygotes. In-silico tool predicts a benign outcome for this variant. 10/13 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
ENST00000520407.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NRG1 | NM_013962.3 | c.473C>T | p.Ala158Val | missense_variant | 1/5 | ||
NRG1 | XM_011544512.3 | c.473C>T | p.Ala158Val | missense_variant | 1/13 | ||
NRG1 | XM_017013367.2 | c.473C>T | p.Ala158Val | missense_variant | 1/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NRG1 | ENST00000520407.5 | c.473C>T | p.Ala158Val | missense_variant | 1/5 | 1 | |||
NRG1 | ENST00000523534.5 | c.32C>T | p.Ala11Val | missense_variant | 1/13 | 5 | |||
NRG1 | ENST00000519301.6 | c.37+1026C>T | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0185 AC: 2804AN: 151916Hom.: 92 Cov.: 32
GnomAD3 exomes AF: 0.00352 AC: 646AN: 183284Hom.: 14 AF XY: 0.00272 AC XY: 278AN XY: 102310
GnomAD4 exome AF: 0.00184 AC: 2601AN: 1414458Hom.: 72 Cov.: 34 AF XY: 0.00157 AC XY: 1100AN XY: 700388
GnomAD4 genome ? AF: 0.0185 AC: 2810AN: 152030Hom.: 92 Cov.: 32 AF XY: 0.0178 AC XY: 1325AN XY: 74324
ClinVar
Submissions by phenotype
NRG1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 12, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at