rs999147
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001323368.2(ST3GAL6):c.336-13A>G variant causes a 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
Genomes: 𝑓 0.36 ( 9795 hom., cov: 32)
Exomes 𝑓: 0.36 ( 97747 hom. )
Consequence
ST3GAL6
NM_001323368.2 intron
NM_001323368.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -3.26
Genes affected
ST3GAL6 (HGNC:18080): (ST3 beta-galactoside alpha-2,3-sialyltransferase 6) The protein encoded by this gene is a member of the sialyltransferase family. Members of this family are enzymes that transfer sialic acid from the activated cytidine 5'-monophospho-N-acetylneuraminic acid to terminal positions on sialylated glycolipids (gangliosides) or to the N- or O-linked sugar chains of glycoproteins. This protein has high specificity for neolactotetraosylceramide and neolactohexaosylceramide as glycolipid substrates and may contribute to the formation of selectin ligands and sialyl Lewis X, a carbohydrate important for cell-to-cell recognition and a blood group antigen. [provided by RefSeq, Apr 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ST3GAL6 | NM_001323368.2 | c.336-13A>G | 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 | intron_variant | 1 | NM_001323368.2 | ENSP00000417376.1 |
Frequencies
GnomAD3 genomes AF: 0.357 AC: 54270AN: 151928Hom.: 9794 Cov.: 32
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GnomAD3 exomes AF: 0.352 AC: 87671AN: 248990Hom.: 15708 AF XY: 0.354 AC XY: 47556AN XY: 134454
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GnomAD4 exome AF: 0.364 AC: 528188AN: 1450494Hom.: 97747 Cov.: 28 AF XY: 0.364 AC XY: 262902AN XY: 721986
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GnomAD4 genome AF: 0.357 AC: 54292AN: 152048Hom.: 9795 Cov.: 32 AF XY: 0.356 AC XY: 26475AN XY: 74298
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at