chr9-127661208-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_ModerateBP6_Very_StrongBS2
The NM_001032221.6(STXBP1):c.429+3G>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 0.0000496 in 1,613,532 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_001032221.6 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
STXBP1 | ENST00000373302.8 | c.429+3G>A | splice_region_variant, intron_variant | 1 | NM_003165.6 | ENSP00000362399.3 | ||||
STXBP1 | ENST00000373299.5 | c.429+3G>A | splice_region_variant, intron_variant | 1 | NM_001032221.6 | ENSP00000362396.2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152130Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000278 AC: 7AN: 251402Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135874
GnomAD4 exome AF: 0.0000527 AC: 77AN: 1461402Hom.: 0 Cov.: 30 AF XY: 0.0000468 AC XY: 34AN XY: 727044
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152130Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74312
ClinVar
Submissions by phenotype
Early infantile epileptic encephalopathy with suppression bursts Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 19, 2024 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | May 18, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at