chr12-124326365-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_006312.6(NCOR2):c.7189G>A(p.Gly2397Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000187 in 1,489,654 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_006312.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NCOR2 | NM_006312.6 | c.7189G>A | p.Gly2397Ser | missense_variant | 48/49 | ENST00000405201.6 | |
NCOR2 | NM_001206654.2 | c.7159G>A | p.Gly2387Ser | missense_variant | 47/48 | ||
NCOR2 | NM_001077261.4 | c.7021G>A | p.Gly2341Ser | missense_variant | 47/48 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NCOR2 | ENST00000405201.6 | c.7189G>A | p.Gly2397Ser | missense_variant | 48/49 | 1 | NM_006312.6 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000959 AC: 146AN: 152196Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.000356 AC: 50AN: 140458Hom.: 1 AF XY: 0.000220 AC XY: 17AN XY: 77306
GnomAD4 exome AF: 0.0000995 AC: 133AN: 1337340Hom.: 0 Cov.: 31 AF XY: 0.0000838 AC XY: 55AN XY: 656514
GnomAD4 genome ? AF: 0.000959 AC: 146AN: 152314Hom.: 1 Cov.: 33 AF XY: 0.000792 AC XY: 59AN XY: 74478
ClinVar
Submissions by phenotype
NCOR2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 10, 2022 | This variant is classified as likely 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