rs2236653
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001254757.2(ST3GAL4):c.916-71C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.437 in 1,557,912 control chromosomes in the GnomAD database, including 150,776 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 0.45 ( 16089 hom., cov: 33)
Exomes 𝑓: 0.44 ( 134687 hom. )
Consequence
ST3GAL4
NM_001254757.2 intron
NM_001254757.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.850
Genes affected
ST3GAL4 (HGNC:10864): (ST3 beta-galactoside alpha-2,3-sialyltransferase 4) This gene encodes a member of the glycosyltransferase 29 family, a group of enzymes involved in protein glycosylation. The encoded protein is targeted to Golgi membranes but may be proteolytically processed and secreted. The gene product may also be involved in the increased expression of sialyl Lewis X antigen seen in inflammatory responses. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]
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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=-0.82).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.663 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ST3GAL4 | NM_001254757.2 | c.916-71C>T | intron_variant | ENST00000444328.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ST3GAL4 | ENST00000444328.7 | c.916-71C>T | intron_variant | 5 | NM_001254757.2 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.454 AC: 69051AN: 151966Hom.: 16069 Cov.: 33
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GnomAD4 exome AF: 0.435 AC: 611582AN: 1405828Hom.: 134687 AF XY: 0.434 AC XY: 304276AN XY: 700520
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GnomAD4 genome ? AF: 0.454 AC: 69114AN: 152084Hom.: 16089 Cov.: 33 AF XY: 0.450 AC XY: 33486AN XY: 74354
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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