rs201145910
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_006772.3(SYNGAP1):c.296-8C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00017 in 1,613,550 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_006772.3 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SYNGAP1 | NM_006772.3 | c.296-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000646630.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SYNGAP1 | ENST00000646630.1 | c.296-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | NM_006772.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000868 AC: 132AN: 152128Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000263 AC: 66AN: 250584Hom.: 0 AF XY: 0.000155 AC XY: 21AN XY: 135490
GnomAD4 exome AF: 0.0000979 AC: 143AN: 1461304Hom.: 0 Cov.: 32 AF XY: 0.0000825 AC XY: 60AN XY: 726952
GnomAD4 genome ? AF: 0.000867 AC: 132AN: 152246Hom.: 0 Cov.: 32 AF XY: 0.000967 AC XY: 72AN XY: 74424
ClinVar
Submissions by phenotype
Intellectual disability, autosomal dominant 5 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 27, 2024 | - - |
SYNGAP1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 30, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 14, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at