rs1569061
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004603.4(STX1A):c.*256G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0795 in 563,168 control chromosomes in the GnomAD database, including 2,230 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.099 ( 941 hom., cov: 32)
Exomes 𝑓: 0.072 ( 1289 hom. )
Consequence
STX1A
NM_004603.4 3_prime_UTR
NM_004603.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0740
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STX1A | NM_004603.4 | c.*256G>A | 3_prime_UTR_variant | 10/10 | ENST00000222812.8 | ||
STX1A | NM_001165903.2 | c.*321G>A | 3_prime_UTR_variant | 10/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STX1A | ENST00000222812.8 | c.*256G>A | 3_prime_UTR_variant | 10/10 | 1 | NM_004603.4 | P1 | ||
STX1A | ENST00000395156.7 | c.*321G>A | 3_prime_UTR_variant | 10/10 | 1 | ||||
STX1A | ENST00000484736.5 | n.536G>A | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0986 AC: 14993AN: 152072Hom.: 934 Cov.: 32
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GnomAD4 exome AF: 0.0724 AC: 29775AN: 410978Hom.: 1289 Cov.: 3 AF XY: 0.0729 AC XY: 15779AN XY: 216400
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GnomAD4 genome ? AF: 0.0987 AC: 15016AN: 152190Hom.: 941 Cov.: 32 AF XY: 0.0976 AC XY: 7265AN XY: 74412
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ClinVar
Not reported inComputational scores
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Name
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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