chr6-147315744-G-A
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_001127715.4(STXBP5):c.1623+9G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000207 in 1,594,916 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Genomes: 𝑓 0.00011 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000012 ( 0 hom. )
Consequence
STXBP5
NM_001127715.4 intron
NM_001127715.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.01
Genes affected
STXBP5 (HGNC:19665): (syntaxin binding protein 5) Syntaxin 1 is a component of the 7S and 20S SNARE complexes which are involved in docking and fusion of synaptic vesicles with the presynaptic plasma membrane. This gene encodes a syntaxin 1 binding protein. In rat, a similar protein dissociates syntaxin 1 from the Munc18/n-Sec1/rbSec1 complex to form a 10S complex, an intermediate which can be converted to the 7S SNARE complex. Thus this protein is thought to be involved in neurotransmitter release by stimulating SNARE complex formation. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
Variant 6-147315744-G-A is Benign according to our data. Variant chr6-147315744-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3052507.Status of the report is no_assertion_criteria_provided, 0 stars.
BS2
High AC in GnomAd4 at 16 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STXBP5 | NM_001127715.4 | c.1623+9G>A | intron_variant | ENST00000321680.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STXBP5 | ENST00000321680.11 | c.1623+9G>A | intron_variant | 5 | NM_001127715.4 | A1 |
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152048Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000483 AC: 12AN: 248284Hom.: 0 AF XY: 0.0000448 AC XY: 6AN XY: 134068
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GnomAD4 exome AF: 0.0000118 AC: 17AN: 1442750Hom.: 0 Cov.: 28 AF XY: 0.0000112 AC XY: 8AN XY: 716236
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GnomAD4 genome AF: 0.000105 AC: 16AN: 152166Hom.: 0 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74398
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
STXBP5-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 13, 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
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Benign
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Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at