chr9-127690612-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_003165.6(STXBP1):c.*17-163C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00372 in 773,436 control chromosomes in the GnomAD database, including 54 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.012 ( 41 hom., cov: 32)
Exomes 𝑓: 0.0018 ( 13 hom. )
Consequence
STXBP1
NM_003165.6 intron
NM_003165.6 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.114
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 Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
?
Variant 9-127690612-C-T is Benign according to our data. Variant chr9-127690612-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 677438.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0117 (1773/152160) while in subpopulation AFR AF= 0.0398 (1650/41480). AF 95% confidence interval is 0.0382. There are 41 homozygotes in gnomad4. There are 846 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 1769 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STXBP1 | NM_001032221.6 | c.1703-163C>T | intron_variant | ENST00000373299.5 | |||
STXBP1 | NM_003165.6 | c.*17-163C>T | intron_variant | ENST00000373302.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STXBP1 | ENST00000373299.5 | c.1703-163C>T | intron_variant | 1 | NM_001032221.6 | A1 | |||
STXBP1 | ENST00000373302.8 | c.*17-163C>T | intron_variant | 1 | NM_003165.6 | P3 | |||
ENST00000624141.1 | n.229G>A | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.0116 AC: 1769AN: 152042Hom.: 41 Cov.: 32
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GnomAD4 exome AF: 0.00178 AC: 1104AN: 621276Hom.: 13 Cov.: 7 AF XY: 0.00138 AC XY: 464AN XY: 335422
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 14, 2018 | 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
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at