rs369625158
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBS1BS2
The NM_003165.6(STXBP1):c.903-4C>G variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000113 in 1,613,892 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Likely benign (★★).
Frequency
Consequence
NM_003165.6 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STXBP1 | NM_001032221.6 | c.903-4C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000373299.5 | |||
STXBP1 | NM_003165.6 | c.903-4C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000373302.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STXBP1 | ENST00000373299.5 | c.903-4C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001032221.6 | A1 | |||
STXBP1 | ENST00000373302.8 | c.903-4C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_003165.6 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.000131 AC: 20AN: 152116Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000756 AC: 19AN: 251456Hom.: 0 AF XY: 0.0000809 AC XY: 11AN XY: 135906
GnomAD4 exome AF: 0.000112 AC: 163AN: 1461776Hom.: 0 Cov.: 31 AF XY: 0.000114 AC XY: 83AN XY: 727192
GnomAD4 genome ? AF: 0.000131 AC: 20AN: 152116Hom.: 0 Cov.: 31 AF XY: 0.000162 AC XY: 12AN XY: 74300
ClinVar
Submissions by phenotype
not specified Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Nov 13, 2015 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 09, 2015 | 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. - |
Early infantile epileptic encephalopathy with suppression bursts Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 28, 2024 | - - |
STXBP1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 25, 2019 | This variant is classified as likely 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