1-235458753-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2PM5PP3
The NM_152490.5(B3GALNT2):c.875G>A(p.Arg292His) variant causes a missense change. The variant allele was found at a frequency of 0.00000625 in 1,600,244 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R292P) has been classified as Likely pathogenic.
Frequency
Consequence
NM_152490.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 151954Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000426 AC: 1AN: 234984Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 126954
GnomAD4 exome AF: 0.00000345 AC: 5AN: 1448172Hom.: 0 Cov.: 33 AF XY: 0.00000417 AC XY: 3AN XY: 719790
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152072Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74338
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at