Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PM2_SupportingBP4_Strong
The NM_001079866.2(BCS1L):c.-49-12C>G variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD Genomes project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
NM_001079866.2 splice_polypyrimidine_tract, intron
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Verdict is Likely_benign. Variant got -3 ACMG points.
GnomAD3 genomesCov.: 33 GnomAD4 exome AF: 0.0000259AC: 37AN: 1427074Hom.: 0 AF XY: 0.0000281AC XY: 20AN XY: 711696
Submissions by phenotype
|Uncertain significance, criteria provided, single submitter
|Oct 14, 2016
|The c.-49-12C>G variant in the BCS1L gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. This variant occurs within a region of the promoter and may alter the splice acceptor site in intron 2. However, in silico analysis is inconsistent in its predictions as to whether or not the variant may affect splicing, and in the absence of functional mRNA studies, the physiological consequence of this variant cannot be precisely determined. Additional data from control individuals in the NHLBI Exome Sequencing Project was not available to assess whether c.-49-12C>G may be a common benign variant in the general population. Therefore, we interpret c.-49-12C>G as a variant of uncertain significance. -
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