chr1-202604508-TCTC-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP3
The NM_177402.5(SYT2):c.289_291delGAG(p.Glu97del) variant causes a conservative inframe deletion change. The variant allele was found at a frequency of 0.00000342 in 1,461,890 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_177402.5 conservative_inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SYT2 | ENST00000367268.5 | c.289_291delGAG | p.Glu97del | conservative_inframe_deletion | Exon 3 of 9 | 1 | NM_177402.5 | ENSP00000356237.4 | ||
SYT2 | ENST00000367267.5 | c.289_291delGAG | p.Glu97del | conservative_inframe_deletion | Exon 3 of 9 | 2 | ENSP00000356236.1 | |||
ENSG00000226862 | ENST00000428573.1 | n.68+176_68+178delCCT | intron_variant | Intron 1 of 1 | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000795 AC: 2AN: 251472Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135902
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461890Hom.: 0 AF XY: 0.00000275 AC XY: 2AN XY: 727244
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Uncertain:1
This variant is present in population databases (no rsID available, gnomAD 0.0009%). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. This variant has not been reported in the literature in individuals affected with SYT2-related conditions. This variant, c.289_291del, results in the deletion of 1 amino acid(s) of the SYT2 protein (p.Glu97del), but otherwise preserves the integrity of the reading frame. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at