X-40055416-T-C
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP3BS2
The NM_001123385.2(BCOR):āc.4693A>Gā(p.Thr1565Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000365 in 1,097,074 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T1565I) has been classified as Uncertain significance.
Frequency
Consequence
NM_001123385.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BCOR | NM_001123385.2 | c.4693A>G | p.Thr1565Ala | missense_variant | 12/15 | ENST00000378444.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BCOR | ENST00000378444.9 | c.4693A>G | p.Thr1565Ala | missense_variant | 12/15 | 1 | NM_001123385.2 | P2 |
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD3 exomes AF: 0.00000545 AC: 1AN: 183481Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67927
GnomAD4 exome AF: 0.00000365 AC: 4AN: 1097074Hom.: 0 Cov.: 30 AF XY: 0.00000552 AC XY: 2AN XY: 362440
GnomAD4 genome Cov.: 23
ClinVar
Submissions by phenotype
Corpus callosum, agenesis of;C0221356:Brachycephaly;C4023628:Mild fetal ventriculomegaly;C4551563:Microcephaly;C5231391:Congenital cerebellar hypoplasia Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Centre for Mendelian Genomics, University Medical Centre Ljubljana | Jan 01, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at