rs10503929
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_013964.5(NRG1):c.866T>C(p.Met289Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 1,613,406 control chromosomes in the GnomAD database, including 22,620 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_013964.5 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_013964.5 | c.866T>C | p.Met289Thr | missense_variant | 9/12 | ENST00000405005.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NRG1 | ENST00000405005.8 | c.866T>C | p.Met289Thr | missense_variant | 9/12 | 1 | NM_013964.5 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.124 AC: 18848AN: 152054Hom.: 1577 Cov.: 32
GnomAD3 exomes AF: 0.131 AC: 32899AN: 250736Hom.: 2843 AF XY: 0.132 AC XY: 17955AN XY: 135526
GnomAD4 exome AF: 0.161 AC: 235965AN: 1461234Hom.: 21043 Cov.: 32 AF XY: 0.160 AC XY: 116229AN XY: 726936
GnomAD4 genome ? AF: 0.124 AC: 18842AN: 152172Hom.: 1577 Cov.: 32 AF XY: 0.124 AC XY: 9232AN XY: 74380
ClinVar
Submissions by phenotype
NRG1-related condition Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 27, 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