22-39381817-C-CCAG
Variant names:
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PM4_Supporting
The NM_004711.5(SYNGR1):c.607_608insGCA(p.Pro202_Thr203insSer) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000026 in 1,460,706 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0 ( 0 hom., cov: 0)
Exomes 𝑓: 0.000026 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
SYNGR1
NM_004711.5 disruptive_inframe_insertion
NM_004711.5 disruptive_inframe_insertion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.13
Genes affected
SYNGR1 (HGNC:11498): (synaptogyrin 1) This gene encodes an integral membrane protein associated with presynaptic vesicles in neuronal cells. The exact function of this protein is unclear, but studies of a similar murine protein suggest that it functions in synaptic plasticity without being required for synaptic transmission. The gene product belongs to the synaptogyrin gene family. Three alternatively spliced variants encoding three different isoforms have been identified. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PM4
Nonframeshift variant in NON repetitive region in NM_004711.5. Strenght limited to Supporting due to length of the change: 1aa.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 151692Hom.: 0 Cov.: 0 FAILED QC
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GnomAD3 exomes AF: 0.0000161 AC: 4AN: 248486Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135042
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GnomAD4 exome AF: 0.0000260 AC: 38AN: 1460706Hom.: 0 Cov.: 37 AF XY: 0.0000275 AC XY: 20AN XY: 726686
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GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 151692Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 74038
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Not reported inComputational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at