chr3-31532766-A-C
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBA1
The ENST00000453168.5(STT3B):n.129A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 614,494 control chromosomes in the GnomAD database, including 12,250 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.19 ( 2881 hom., cov: 33)
Exomes 𝑓: 0.20 ( 9369 hom. )
Consequence
STT3B
ENST00000453168.5 non_coding_transcript_exon
ENST00000453168.5 non_coding_transcript_exon
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0210
Genes affected
STT3B (HGNC:30611): (STT3 oligosaccharyltransferase complex catalytic subunit B) The protein encoded by this gene is a catalytic subunit of a protein complex that transfers oligosaccharides onto asparagine residues. Defects in this gene are a cause of congenital disorder of glycosylation Ix (CDG1X). [provided by RefSeq, Jun 2014]
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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=-0.34).
BP6
?
Variant 3-31532766-A-C is Benign according to our data. Variant chr3-31532766-A-C is described in ClinVar as [Benign]. Clinvar id is 1292289.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.252 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STT3B | ENST00000453168.5 | n.129A>C | non_coding_transcript_exon_variant | 1/10 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.190 AC: 28814AN: 151704Hom.: 2880 Cov.: 33
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GnomAD4 exome AF: 0.199 AC: 92105AN: 462670Hom.: 9369 Cov.: 7 AF XY: 0.200 AC XY: 47312AN XY: 237118
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GnomAD4 genome ? AF: 0.190 AC: 28822AN: 151824Hom.: 2881 Cov.: 33 AF XY: 0.190 AC XY: 14080AN XY: 74200
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 29, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at