rs2146825290
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2
The NM_001123385.2(BCOR):c.5189C>T(p.Thr1730Met) variant causes a missense change. The variant allele was found at a frequency of 0.00000273 in 1,097,088 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. T1730T) has been classified as Benign.
Frequency
Consequence
NM_001123385.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Our verdict: Likely_benign. The variant received -4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 24
GnomAD4 exome AF: 0.00000273 AC: 3AN: 1097088Hom.: 0 Cov.: 30 AF XY: 0.00000552 AC XY: 2AN XY: 362490 show subpopulations
GnomAD4 genome Cov.: 24
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.5189C>T (p.T1730M) alteration is located in exon 15 (coding exon 14) of the BCOR gene. This alteration results from a C to T substitution at nucleotide position 5189, causing the threonine (T) at amino acid position 1730 to be replaced by a methionine (M). 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