chr7-73700443-G-A
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_004603.4(STX1A):c.831C>T(p.Ile277=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000805 in 1,613,950 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 (★).
Frequency
Genomes: 𝑓 0.00020 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000068 ( 0 hom. )
Consequence
STX1A
NM_004603.4 synonymous
NM_004603.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.01
Genes affected
STX1A (HGNC:11433): (syntaxin 1A) This gene encodes a member of the syntaxin superfamily. Syntaxins are nervous system-specific proteins implicated in the docking of synaptic vesicles with the presynaptic plasma membrane. Syntaxins possess a single C-terminal transmembrane domain, a SNARE [Soluble NSF (N-ethylmaleimide-sensitive fusion protein)-Attachment protein REceptor] domain (known as H3), and an N-terminal regulatory domain (Habc). Syntaxins bind synaptotagmin in a calcium-dependent fashion and interact with voltage dependent calcium and potassium channels via the C-terminal H3 domain. This gene product is a key molecule in ion channel regulation and synaptic exocytosis. Alternatively spliced transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Sep 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.51).
BP6
Variant 7-73700443-G-A is Benign according to our data. Variant chr7-73700443-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3044853.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-1.01 with no splicing effect.
BS2
High AC in GnomAd4 at 30 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STX1A | NM_004603.4 | c.831C>T | p.Ile277= | synonymous_variant | 10/10 | ENST00000222812.8 | |
STX1A | NM_001165903.2 | c.*29C>T | 3_prime_UTR_variant | 10/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STX1A | ENST00000222812.8 | c.831C>T | p.Ile277= | synonymous_variant | 10/10 | 1 | NM_004603.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000197 AC: 30AN: 152086Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.0000479 AC: 12AN: 250760Hom.: 0 AF XY: 0.0000443 AC XY: 6AN XY: 135592
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GnomAD4 exome AF: 0.0000684 AC: 100AN: 1461864Hom.: 0 Cov.: 31 AF XY: 0.0000591 AC XY: 43AN XY: 727242
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GnomAD4 genome AF: 0.000197 AC: 30AN: 152086Hom.: 0 Cov.: 31 AF XY: 0.000162 AC XY: 12AN XY: 74288
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
STX1A-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 28, 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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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at