rs10496407
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001142351.2(ST6GAL2):c.*2991G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.359 in 151,952 control chromosomes in the GnomAD database, including 10,762 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 ( 10762 hom., cov: 32)
Failed GnomAD Quality Control
Consequence
ST6GAL2
NM_001142351.2 3_prime_UTR
NM_001142351.2 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.09
Genes affected
ST6GAL2 (HGNC:10861): (ST6 beta-galactoside alpha-2,6-sialyltransferase 2) This locus encodes a sialyltransferase. The encoded type II transmembrane protein catalyzes the transfer of sialic acid from CMP to an oligosaccharide substrate. Polymorphisms at this locus may be associated with variations in risperidone response in schizophrenic patients. Alternatively spliced transcript variants have been described. [provided by RefSeq, Jan 2012]
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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=-0.9).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ST6GAL2 | NM_001142351.2 | c.*2991G>A | 3_prime_UTR_variant | 6/6 | ENST00000409382.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ST6GAL2 | ENST00000409382.8 | c.*2991G>A | 3_prime_UTR_variant | 6/6 | 1 | NM_001142351.2 | P1 | ||
ST6GAL2 | ENST00000361686.8 | c.*2991G>A | 3_prime_UTR_variant | 6/6 | 1 | P1 | |||
ST6GAL2 | ENST00000361803.3 | c.*33-1824G>A | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.359 AC: 54460AN: 151834Hom.: 10761 Cov.: 32
GnomAD3 genomes
?
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32
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GnomAD4 exome Data not reliable, filtered out with message: AC0AC: 0AN: 0Hom.: 0 Cov.: 0AC XY: 0AN XY: 0
GnomAD4 exome
Data not reliable, filtered out with message: AC0
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GnomAD4 genome ? AF: 0.359 AC: 54484AN: 151952Hom.: 10762 Cov.: 32 AF XY: 0.349 AC XY: 25882AN XY: 74232
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3476
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at