12-122206519-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_030765.4(B3GNT4):c.268C>T(p.Pro90Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00000274 in 1,461,878 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_030765.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
B3GNT4 | NM_030765.4 | c.268C>T | p.Pro90Ser | missense_variant | Exon 3 of 3 | ENST00000324189.5 | NP_110392.1 | |
B3GNT4 | NM_001330492.2 | c.193C>T | p.Pro65Ser | missense_variant | Exon 2 of 2 | NP_001317421.1 | ||
B3GNT4 | XM_047429535.1 | c.193C>T | p.Pro65Ser | missense_variant | Exon 2 of 2 | XP_047285491.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251464Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135910
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461878Hom.: 0 Cov.: 30 AF XY: 0.00000413 AC XY: 3AN XY: 727244
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.268C>T (p.P90S) alteration is located in exon 3 (coding exon 2) of the B3GNT4 gene. This alteration results from a C to T substitution at nucleotide position 268, causing the proline (P) at amino acid position 90 to be replaced by a serine (S). 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