rs76400963
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_178862.3(STT3B):c.777+7T>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0139 in 1,606,354 control chromosomes in the GnomAD database, including 227 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_178862.3 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STT3B | NM_178862.3 | c.777+7T>G | splice_region_variant, intron_variant | ENST00000295770.4 | |||
STT3B | XM_011533465.2 | c.777+7T>G | splice_region_variant, intron_variant | ||||
STT3B | XM_017005858.2 | c.339+7T>G | splice_region_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STT3B | ENST00000295770.4 | c.777+7T>G | splice_region_variant, intron_variant | 1 | NM_178862.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0125 AC: 1898AN: 152162Hom.: 20 Cov.: 32
GnomAD3 exomes AF: 0.0133 AC: 3321AN: 249996Hom.: 46 AF XY: 0.0136 AC XY: 1831AN XY: 135114
GnomAD4 exome AF: 0.0141 AC: 20457AN: 1454074Hom.: 207 Cov.: 28 AF XY: 0.0140 AC XY: 10105AN XY: 723822
GnomAD4 genome ? AF: 0.0125 AC: 1898AN: 152280Hom.: 20 Cov.: 32 AF XY: 0.0124 AC XY: 925AN XY: 74452
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 12, 2016 | 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
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
STT3B-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 23, 2024 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at