3-98726480-A-G
Variant names:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000461931.1(ST3GAL6-AS1):n.226+5946T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.529 in 152,112 control chromosomes in the GnomAD database, including 22,077 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 0.53 ( 22077 hom., cov: 33)
Consequence
ST3GAL6-AS1
ENST00000461931.1 intron
ENST00000461931.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.227
Genes affected
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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=-0.94).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.664 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ST3GAL6-AS1 | NR_046683.1 | n.226+5946T>C | intron_variant | Intron 1 of 4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ST3GAL6-AS1 | ENST00000461931.1 | n.226+5946T>C | intron_variant | Intron 1 of 3 | 2 | |||||
ST3GAL6-AS1 | ENST00000475816.5 | n.83+5946T>C | intron_variant | Intron 1 of 3 | 3 | |||||
ST3GAL6-AS1 | ENST00000488132.6 | n.82+5946T>C | intron_variant | Intron 1 of 5 | 3 |
Frequencies
GnomAD3 genomes AF: 0.528 AC: 80296AN: 151994Hom.: 22037 Cov.: 33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.529 AC: 80395AN: 152112Hom.: 22077 Cov.: 33 AF XY: 0.527 AC XY: 39228AN XY: 74374
GnomAD4 genome
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at