rs143697110
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_ModerateBP6_Very_StrongBS2
The NM_001123385.2(BCOR):c.626C>T(p.Ser209Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000963 in 1,209,771 control chromosomes in the GnomAD database, including 2 homozygotes. There are 382 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. S209S) has been classified as Likely benign.
Frequency
Consequence
NM_001123385.2 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 |
---|---|---|---|---|---|---|---|
BCOR | NM_001123385.2 | c.626C>T | p.Ser209Leu | missense_variant | 4/15 | ENST00000378444.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BCOR | ENST00000378444.9 | c.626C>T | p.Ser209Leu | missense_variant | 4/15 | 1 | NM_001123385.2 | P2 |
Frequencies
GnomAD3 genomes AF: 0.000744 AC: 83AN: 111561Hom.: 0 Cov.: 23 AF XY: 0.000711 AC XY: 24AN XY: 33739
GnomAD3 exomes AF: 0.000583 AC: 107AN: 183508Hom.: 0 AF XY: 0.000662 AC XY: 45AN XY: 67938
GnomAD4 exome AF: 0.000985 AC: 1082AN: 1098160Hom.: 2 Cov.: 35 AF XY: 0.000985 AC XY: 358AN XY: 363514
GnomAD4 genome AF: 0.000744 AC: 83AN: 111611Hom.: 0 Cov.: 23 AF XY: 0.000710 AC XY: 24AN XY: 33799
ClinVar
Submissions by phenotype
not specified Benign:2Other:1
Benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
Benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
not provided Benign:2
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) | - | - - |
Inborn genetic diseases Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 26, 2024 | This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Oculofaciocardiodental syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 14, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at