rs999147
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000483910.6(ST3GAL6):c.336-13A>G variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.363 in 1,602,542 control chromosomes in the GnomAD database, including 107,542 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
ENST00000483910.6 splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ST3GAL6 | NM_001323368.2 | c.336-13A>G | splice_polypyrimidine_tract_variant, intron_variant | ENST00000483910.6 | NP_001310297.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ST3GAL6 | ENST00000483910.6 | c.336-13A>G | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001323368.2 | ENSP00000417376 | P1 |
Frequencies
GnomAD3 genomes AF: 0.357 AC: 54270AN: 151928Hom.: 9794 Cov.: 32
GnomAD3 exomes AF: 0.352 AC: 87671AN: 248990Hom.: 15708 AF XY: 0.354 AC XY: 47556AN XY: 134454
GnomAD4 exome AF: 0.364 AC: 528188AN: 1450494Hom.: 97747 Cov.: 28 AF XY: 0.364 AC XY: 262902AN XY: 721986
GnomAD4 genome AF: 0.357 AC: 54292AN: 152048Hom.: 9795 Cov.: 32 AF XY: 0.356 AC XY: 26475AN XY: 74298
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at