12-124336867-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_006312.6(NCOR2):c.6001C>T(p.Pro2001Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0457 in 1,611,108 control chromosomes in the GnomAD database, including 2,192 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/19 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_006312.6 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 |
---|---|---|---|---|---|---|---|
NCOR2 | NM_006312.6 | c.6001C>T | p.Pro2001Ser | missense_variant | 40/49 | ENST00000405201.6 | |
NCOR2 | NM_001206654.2 | c.5971C>T | p.Pro1991Ser | missense_variant | 39/48 | ||
NCOR2 | NM_001077261.4 | c.5971C>T | p.Pro1991Ser | missense_variant | 39/48 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NCOR2 | ENST00000405201.6 | c.6001C>T | p.Pro2001Ser | missense_variant | 40/49 | 1 | NM_006312.6 | P4 | |
NCOR2 | ENST00000429285.6 | c.5971C>T | p.Pro1991Ser | missense_variant | 38/47 | 1 | A2 | ||
NCOR2 | ENST00000404621.5 | c.5971C>T | p.Pro1991Ser | missense_variant | 38/47 | 1 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0449 AC: 6834AN: 152154Hom.: 173 Cov.: 33
GnomAD3 exomes AF: 0.0466 AC: 11316AN: 242918Hom.: 400 AF XY: 0.0510 AC XY: 6762AN XY: 132530
GnomAD4 exome AF: 0.0458 AC: 66758AN: 1458836Hom.: 2020 Cov.: 31 AF XY: 0.0481 AC XY: 34928AN XY: 725704
GnomAD4 genome AF: 0.0449 AC: 6844AN: 152272Hom.: 172 Cov.: 33 AF XY: 0.0457 AC XY: 3402AN XY: 74448
ClinVar
Submissions by phenotype
NCOR2-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 20, 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