9-127660064-C-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 3P and 16B. PM1PP2BP4_StrongBP6_Very_StrongBS2
The NM_001032221.6(STXBP1):c.281C>T(p.Pro94Leu) variant causes a missense change. The variant allele was found at a frequency of 0.000284 in 1,614,090 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. P94P) has been classified as Likely benign.
Frequency
Consequence
NM_001032221.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
STXBP1 | ENST00000373302.8 | c.281C>T | p.Pro94Leu | missense_variant | Exon 5 of 20 | 1 | NM_003165.6 | ENSP00000362399.3 | ||
STXBP1 | ENST00000373299.5 | c.281C>T | p.Pro94Leu | missense_variant | Exon 5 of 19 | 1 | NM_001032221.6 | ENSP00000362396.2 |
Frequencies
GnomAD3 genomes AF: 0.000151 AC: 23AN: 152098Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000537 AC: 135AN: 251484Hom.: 0 AF XY: 0.000728 AC XY: 99AN XY: 135916
GnomAD4 exome AF: 0.000298 AC: 436AN: 1461874Hom.: 4 Cov.: 31 AF XY: 0.000428 AC XY: 311AN XY: 727238
GnomAD4 genome AF: 0.000151 AC: 23AN: 152216Hom.: 0 Cov.: 32 AF XY: 0.000242 AC XY: 18AN XY: 74412
ClinVar
Submissions by phenotype
not provided Benign:3
STXBP1: PP2, BS1, BS2 -
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Inborn genetic diseases Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Early infantile epileptic encephalopathy with suppression bursts Benign:1
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STXBP1-related disorder Benign:1
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). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at