chrX-40073567-G-T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_001123385.2(BCOR):c.1779C>A(p.Ser593=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00305 in 1,211,089 control chromosomes in the GnomAD database, including 55 homozygotes. There are 1,077 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. S593S) has been classified as Likely benign.
Frequency
Consequence
NM_001123385.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BCOR | NM_001123385.2 | c.1779C>A | p.Ser593= | synonymous_variant | 4/15 | ENST00000378444.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BCOR | ENST00000378444.9 | c.1779C>A | p.Ser593= | synonymous_variant | 4/15 | 1 | NM_001123385.2 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0142 AC: 1608AN: 113066Hom.: 20 Cov.: 25 AF XY: 0.0138 AC XY: 485AN XY: 35200
GnomAD3 exomes AF: 0.00484 AC: 886AN: 182959Hom.: 13 AF XY: 0.00360 AC XY: 243AN XY: 67457
GnomAD4 exome AF: 0.00190 AC: 2084AN: 1097970Hom.: 35 Cov.: 31 AF XY: 0.00162 AC XY: 587AN XY: 363362
GnomAD4 genome ? AF: 0.0143 AC: 1612AN: 113119Hom.: 20 Cov.: 25 AF XY: 0.0139 AC XY: 490AN XY: 35263
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Genetic Services Laboratory, University of Chicago | - | Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 31, 2018 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
History of neurodevelopmental disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 11, 2014 | General population or subpopulation frequency is too high to be a pathogenic mutation based on disease/syndrome prevalence and penetrance - |
Oculofaciocardiodental syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 15, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at