X-47573994-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_006950.3(SYN1):c.1982+8G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000265 in 1,129,993 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. 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_006950.3 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SYN1 | ENST00000295987.13 | c.1982+8G>A | splice_region_variant, intron_variant | Intron 12 of 12 | 2 | NM_006950.3 | ENSP00000295987.7 | |||
SYN1 | ENST00000340666.5 | c.1982+8G>A | splice_region_variant, intron_variant | Intron 12 of 12 | 1 | ENSP00000343206.4 | ||||
SYN1 | ENST00000640721.1 | c.70+694G>A | intron_variant | Intron 1 of 1 | 5 | ENSP00000492857.1 |
Frequencies
GnomAD3 genomes AF: 0.00000891 AC: 1AN: 112258Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34456
GnomAD4 exome AF: 0.00000197 AC: 2AN: 1017735Hom.: 0 Cov.: 31 AF XY: 0.00000308 AC XY: 1AN XY: 324879
GnomAD4 genome AF: 0.00000891 AC: 1AN: 112258Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34456
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at