chr12-124325431-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_006312.6(NCOR2):c.7516C>A(p.Gln2506Lys) variant causes a missense change. The variant allele was found at a frequency of 0.0000075 in 133,292 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Q2506L) has been classified as Uncertain significance.
Frequency
Consequence
NM_006312.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NCOR2 | NM_006312.6 | c.7516C>A | p.Gln2506Lys | missense_variant | 49/49 | ENST00000405201.6 | |
NCOR2 | NM_001206654.2 | c.7486C>A | p.Gln2496Lys | missense_variant | 48/48 | ||
NCOR2 | NM_001077261.4 | c.7348C>A | p.Gln2450Lys | missense_variant | 48/48 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NCOR2 | ENST00000405201.6 | c.7516C>A | p.Gln2506Lys | missense_variant | 49/49 | 1 | NM_006312.6 | P4 |
Frequencies
GnomAD3 genomes AF: 0.00000750 AC: 1AN: 133292Hom.: 0 Cov.: 29
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1131210Hom.: 0 Cov.: 39 AF XY: 0.00 AC XY: 0AN XY: 547194
GnomAD4 genome AF: 0.00000750 AC: 1AN: 133292Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 63136
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 08, 2023 | The c.7516C>A (p.Q2506K) alteration is located in exon 49 (coding exon 47) of the NCOR2 gene. This alteration results from a C to A substitution at nucleotide position 7516, causing the glutamine (Q) at amino acid position 2506 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at