chr3-31533043-C-T
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_178862.3(STT3B):c.45C>T(p.Leu15=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000063 in 1,586,984 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000056 ( 0 hom. )
Consequence
STT3B
NM_178862.3 synonymous
NM_178862.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.958
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 Likely_benign. Variant got -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.57).
BP6
Variant 3-31533043-C-T is Benign according to our data. Variant chr3-31533043-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 506931.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.958 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STT3B | NM_178862.3 | c.45C>T | p.Leu15= | synonymous_variant | 1/16 | ENST00000295770.4 | |
STT3B | XM_011533465.2 | c.45C>T | p.Leu15= | synonymous_variant | 1/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STT3B | ENST00000295770.4 | c.45C>T | p.Leu15= | synonymous_variant | 1/16 | 1 | NM_178862.3 | P1 | |
STT3B | ENST00000453168.5 | n.406C>T | non_coding_transcript_exon_variant | 1/10 | 1 | ||||
STT3B | ENST00000423527.5 | n.72C>T | non_coding_transcript_exon_variant | 1/10 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151842Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000143 AC: 3AN: 209792Hom.: 0 AF XY: 0.0000256 AC XY: 3AN XY: 117000
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GnomAD4 exome AF: 0.00000557 AC: 8AN: 1435142Hom.: 0 Cov.: 32 AF XY: 0.00000980 AC XY: 7AN XY: 713928
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GnomAD4 genome AF: 0.0000132 AC: 2AN: 151842Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74158
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 24, 2017 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at