rs80055718
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_006279.5(ST3GAL3):c.892-9G>A 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 0.0579 in 1,614,058 control chromosomes in the GnomAD database, including 3,083 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.043 ( 211 hom., cov: 32)
Exomes 𝑓: 0.059 ( 2872 hom. )
Consequence
ST3GAL3
NM_006279.5 splice_polypyrimidine_tract, intron
NM_006279.5 splice_polypyrimidine_tract, intron
Scores
2
Splicing: ADA: 0.0001221
2
Clinical Significance
Conservation
PhyloP100: -1.45
Genes affected
ST3GAL3 (HGNC:10866): (ST3 beta-galactoside alpha-2,3-sialyltransferase 3) The protein encoded by this gene is a type II membrane protein that catalyzes the transfer of sialic acid from CMP-sialic acid to galactose-containing substrates. The encoded protein is normally found in the Golgi apparatus but can be proteolytically processed to a soluble form. This protein is a member of glycosyltransferase family 29. Mutations in this gene have been associated with a form of autosomal recessive nonsymdromic cognitive disability as well as infantile epileptic encephalopathy. Multiple transcript variants encoding several different isoforms have been found for this gene. [provided by RefSeq, Jul 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
Variant 1-43920773-G-A is Benign according to our data. Variant chr1-43920773-G-A is described in ClinVar as [Benign]. Clinvar id is 130375.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0652 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ST3GAL3 | NM_006279.5 | c.892-9G>A | splice_polypyrimidine_tract_variant, intron_variant | ENST00000347631.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ST3GAL3 | ENST00000347631.8 | c.892-9G>A | splice_polypyrimidine_tract_variant, intron_variant | 5 | NM_006279.5 | A1 |
Frequencies
GnomAD3 genomes AF: 0.0434 AC: 6605AN: 152090Hom.: 209 Cov.: 32
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GnomAD3 exomes AF: 0.0457 AC: 11465AN: 251112Hom.: 345 AF XY: 0.0466 AC XY: 6325AN XY: 135738
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GnomAD4 exome AF: 0.0595 AC: 86915AN: 1461850Hom.: 2872 Cov.: 37 AF XY: 0.0588 AC XY: 42765AN XY: 727228
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GnomAD4 genome AF: 0.0435 AC: 6614AN: 152208Hom.: 211 Cov.: 32 AF XY: 0.0423 AC XY: 3150AN XY: 74402
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ClinVar
Significance: Benign
Submissions summary: Benign:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:3
Likely benign, no assertion criteria provided | clinical testing | Genetic Services Laboratory, University of Chicago | - | Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Jun 14, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Early infantile epileptic encephalopathy with suppression bursts Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 04, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at