3-31533139-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 2P and 11B. PM2BP4_ModerateBP6_Very_StrongBP7
The NM_178862.3(STT3B):c.141C>T(p.Gly47Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000196 in 1,295,966 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
Consequence
NM_178862.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
STT3B | ENST00000295770.4 | c.141C>T | p.Gly47Gly | synonymous_variant | Exon 1 of 16 | 1 | NM_178862.3 | ENSP00000295770.2 | ||
STT3B | ENST00000453168.5 | n.502C>T | non_coding_transcript_exon_variant | Exon 1 of 10 | 1 | |||||
STT3B | ENST00000423527.5 | n.168C>T | non_coding_transcript_exon_variant | Exon 1 of 10 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00102 AC: 154AN: 151228Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000193 AC: 3AN: 15558Hom.: 0 AF XY: 0.000119 AC XY: 1AN XY: 8372
GnomAD4 exome AF: 0.0000874 AC: 100AN: 1144632Hom.: 0 Cov.: 32 AF XY: 0.0000834 AC XY: 46AN XY: 551856
GnomAD4 genome AF: 0.00102 AC: 154AN: 151334Hom.: 0 Cov.: 32 AF XY: 0.000933 AC XY: 69AN XY: 73938
ClinVar
Submissions by phenotype
not specified Benign:1
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. -
STT3B-congenital disorder of glycosylation Benign:1
- -
not provided Benign:1
STT3B: BP4, BP7 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at