9-127612242-G-GCTCGCGCCGCGCC
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The ENST00000637953.1(STXBP1):c.-160_-148dup variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0014 in 589,374 control chromosomes in the GnomAD database, including 5 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0050 ( 4 hom., cov: 30)
Exomes 𝑓: 0.00019 ( 1 hom. )
Consequence
STXBP1
ENST00000637953.1 5_prime_UTR
ENST00000637953.1 5_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.505
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 -10 ACMG points.
BP6
?
Variant 9-127612242-G-GCTCGCGCCGCGCC is Benign according to our data. Variant chr9-127612242-G-GCTCGCGCCGCGCC is described in ClinVar as [Likely_benign]. Clinvar id is 1195695.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.005 (739/147738) while in subpopulation AFR AF= 0.0167 (682/40902). AF 95% confidence interval is 0.0156. There are 4 homozygotes in gnomad4. There are 354 alleles in male gnomad4 subpopulation. Median coverage is 30. This position pass quality control queck.
BS2
?
High AC in GnomAd at 738 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STXBP1 | NM_001032221.6 | upstream_gene_variant | ENST00000373299.5 | ||||
STXBP1 | NM_003165.6 | upstream_gene_variant | ENST00000373302.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STXBP1 | ENST00000373299.5 | upstream_gene_variant | 1 | NM_001032221.6 | A1 | ||||
STXBP1 | ENST00000373302.8 | upstream_gene_variant | 1 | NM_003165.6 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.00500 AC: 738AN: 147628Hom.: 4 Cov.: 30
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GnomAD4 exome AF: 0.000195 AC: 86AN: 441636Hom.: 1 Cov.: 8 AF XY: 0.000179 AC XY: 40AN XY: 223806
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GnomAD4 genome ? AF: 0.00500 AC: 739AN: 147738Hom.: 4 Cov.: 30 AF XY: 0.00492 AC XY: 354AN XY: 71998
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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 | Jul 27, 2018 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at