chr11-62615806-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_012200.4(B3GAT3):c.910-7G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,122 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_012200.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
B3GAT3 | ENST00000265471.10 | c.910-7G>A | splice_region_variant, intron_variant | Intron 4 of 4 | 1 | NM_012200.4 | ENSP00000265471.5 | |||
B3GAT3 | ENST00000532585.5 | n.*1032-7G>A | splice_region_variant, intron_variant | Intron 5 of 5 | 1 | ENSP00000432604.1 | ||||
B3GAT3 | ENST00000531383 | c.*380G>A | 3_prime_UTR_variant | Exon 5 of 5 | 2 | ENSP00000431359.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000806 AC: 2AN: 248148Hom.: 0 AF XY: 0.00000744 AC XY: 1AN XY: 134422
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461122Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 726848
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Larsen-like syndrome, B3GAT3 type Uncertain:1
This sequence change falls in intron 4 of the B3GAT3 gene. It does not directly change the encoded amino acid sequence of the B3GAT3 protein. This variant is present in population databases (rs778227646, gnomAD 0.002%). This variant has not been reported in the literature in individuals affected with B3GAT3-related conditions. ClinVar contains an entry for this variant (Variation ID: 1407344). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at