rs2307973
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
The NM_133625.6(SYN2):c.1613+405_1613+406del variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.73 ( 36795 hom., cov: 0)
Consequence
SYN2
NM_133625.6 intron
NM_133625.6 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.614
Genes affected
SYN2 (HGNC:11495): (synapsin II) This gene is a member of the synapsin gene family. Synapsins encode neuronal phosphoproteins which associate with the cytoplasmic surface of synaptic vesicles. Family members are characterized by common protein domains, and they are implicated in synaptogenesis and the modulation of neurotransmitter release, suggesting a potential role in several neuropsychiatric diseases. This member of the synapsin family encodes a neuron-specific phosphoprotein that selectively binds to small synaptic vesicles in the presynaptic nerve terminal. Polymorphisms in this gene are associated with abnormal presynaptic function and related neuronal disorders, including autism, epilepsy, bipolar disorder and schizophrenia. Alternative splicing of this gene results in multiple transcript variants. The tissue inhibitor of metalloproteinase 4 gene is located within an intron of this gene and is transcribed in the opposite direction. [provided by RefSeq, Feb 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.788 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SYN2 | NM_133625.6 | c.1613+405_1613+406del | intron_variant | ENST00000621198.5 | |||
SYN2 | XM_006713312.5 | c.1130+405_1130+406del | intron_variant | ||||
SYN2 | XM_006713313.3 | c.842+405_842+406del | intron_variant | ||||
SYN2 | XM_017007087.2 | c.941+405_941+406del | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SYN2 | ENST00000621198.5 | c.1613+405_1613+406del | intron_variant | 1 | NM_133625.6 | P2 | |||
ENST00000690965.1 | n.527+4351_527+4352del | intron_variant, non_coding_transcript_variant | |||||||
SYN2 | ENST00000439861.5 | n.1232+405_1232+406del | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.726 AC: 104166AN: 143558Hom.: 36762 Cov.: 0
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.726 AC: 104248AN: 143676Hom.: 36795 Cov.: 0 AF XY: 0.729 AC XY: 51229AN XY: 70282
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3478
ClinVar
Not reported inComputational scores
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at