rs556763394
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001374309.2(STXBP1):c.-6+197_-6+209delTCGCGCCGCGCCC variant causes a intron change. The variant allele was found at a frequency of 0.00000226 in 441,642 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 30)
Exomes 𝑓: 0.0000023 ( 0 hom. )
Consequence
STXBP1
NM_001374309.2 intron
NM_001374309.2 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 4.91
Genes affected
STXBP1 (HGNC:11444): (syntaxin binding protein 1) This gene encodes a syntaxin-binding protein. The encoded protein appears to play a role in release of neurotransmitters via regulation of syntaxin, a transmembrane attachment protein receptor. Mutations in this gene have been associated with infantile epileptic encephalopathy-4. Alternatively spliced transcript variants have been described. [provided by RefSeq, Feb 2010]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
STXBP1 | ENST00000373302.8 | c.-161_-149delCTCGCGCCGCGCC | upstream_gene_variant | 1 | NM_003165.6 | ENSP00000362399.3 | ||||
STXBP1 | ENST00000373299.5 | c.-161_-149delCTCGCGCCGCGCC | upstream_gene_variant | 1 | NM_001032221.6 | ENSP00000362396.2 |
Frequencies
GnomAD3 genomes Cov.: 30
GnomAD3 genomes
Cov.:
30
GnomAD4 exome AF: 0.00000226 AC: 1AN: 441642Hom.: 0 AF XY: 0.00000447 AC XY: 1AN XY: 223808
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GnomAD4 genome Cov.: 30
GnomAD4 genome
Cov.:
30
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.