rs1262952349
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 5P and 4B. PM2PM5PP2BP4_ModerateBP6_Moderate
The NM_003165.6(STXBP1):c.25G>A(p.Val9Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000138 in 1,445,708 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V9L?) has been classified as Pathogenic.
Frequency
Consequence
NM_003165.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STXBP1 | NM_003165.6 | c.25G>A | p.Val9Ile | missense_variant | 1/20 | ENST00000373302.8 | |
STXBP1 | NM_001032221.6 | c.25G>A | p.Val9Ile | missense_variant | 1/19 | ENST00000373299.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STXBP1 | ENST00000373302.8 | c.25G>A | p.Val9Ile | missense_variant | 1/20 | 1 | NM_003165.6 | P3 | |
STXBP1 | ENST00000373299.5 | c.25G>A | p.Val9Ile | missense_variant | 1/19 | 1 | NM_001032221.6 | A1 |
Frequencies
GnomAD3 genomes ? Cov.: 30
GnomAD3 exomes AF: 0.00000437 AC: 1AN: 229032Hom.: 0 AF XY: 0.00000795 AC XY: 1AN XY: 125798
GnomAD4 exome AF: 0.00000138 AC: 2AN: 1445708Hom.: 0 Cov.: 31 AF XY: 0.00000139 AC XY: 1AN XY: 719104
GnomAD4 genome ? Cov.: 30
ClinVar
Submissions by phenotype
Early infantile epileptic encephalopathy with suppression bursts Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 21, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at