6-33446569-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_006772.3(SYNGAP1):c.3583-6G>C variant causes a splice region, intron change. The variant allele was found at a frequency of 0.000000684 in 1,461,348 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_006772.3 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SYNGAP1 | NM_006772.3 | c.3583-6G>C | splice_region_variant, intron_variant | Intron 16 of 18 | ENST00000646630.1 | NP_006763.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SYNGAP1 | ENST00000646630.1 | c.3583-6G>C | splice_region_variant, intron_variant | Intron 16 of 18 | NM_006772.3 | ENSP00000496007.1 | ||||
SYNGAP1 | ENST00000644458.1 | c.3583-6G>C | splice_region_variant, intron_variant | Intron 16 of 18 | ENSP00000495541.1 | |||||
SYNGAP1 | ENST00000449372.7 | c.3541-12G>C | intron_variant | Intron 15 of 17 | 5 | ENSP00000416519.4 | ||||
SYNGAP1 | ENST00000418600.7 | c.3583-6G>C | splice_region_variant, intron_variant | Intron 16 of 18 | 5 | ENSP00000403636.3 | ||||
SYNGAP1 | ENST00000645250.1 | c.3406-6G>C | splice_region_variant, intron_variant | Intron 14 of 16 | ENSP00000494861.1 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250906Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135684
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461348Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 726960
GnomAD4 genome Cov.: 31
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at