chr16-30989353-A-AG
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_052874.5(STX1B):c.*3467_*3468insC variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00155 in 149,694 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.0015 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
STX1B
NM_052874.5 3_prime_UTR
NM_052874.5 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.450
Genes affected
STX1B (HGNC:18539): (syntaxin 1B) The protein encoded by this gene belongs to a family of proteins thought to play a role in the exocytosis of synaptic vesicles. Vesicle exocytosis releases vesicular contents and is important to various cellular functions. For instance, the secretion of transmitters from neurons plays an important role in synaptic transmission. After exocytosis, the membrane and proteins from the vesicle are retrieved from the plasma membrane through the process of endocytosis. Mutations in this gene have been identified as one cause of fever-associated epilepsy syndromes. A possible link between this gene and Parkinson's disease has also been suggested. [provided by RefSeq, Jan 2015]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BS2
High AC in GnomAd4 at 232 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STX1B | NM_052874.5 | c.*3467_*3468insC | 3_prime_UTR_variant | 10/10 | ENST00000215095.11 | ||
STX1B | XM_017022893.2 | c.*3467_*3468insC | 3_prime_UTR_variant | 10/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STX1B | ENST00000215095.11 | c.*3467_*3468insC | 3_prime_UTR_variant | 10/10 | 1 | NM_052874.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00155 AC: 232AN: 149576Hom.: 0 Cov.: 32
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GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 60Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 38
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GnomAD4 genome AF: 0.00155 AC: 232AN: 149694Hom.: 0 Cov.: 32 AF XY: 0.00134 AC XY: 98AN XY: 73064
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Neonatal hemochromatosis Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Oxford Medical Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust | Mar 23, 2023 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at