9-127612401-G-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_001032221.6(STXBP1):c.-3G>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000107 in 1,595,014 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001032221.6 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000395 AC: 6AN: 151838Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000178 AC: 4AN: 225232Hom.: 0 AF XY: 0.00000808 AC XY: 1AN XY: 123736
GnomAD4 exome AF: 0.00000762 AC: 11AN: 1443176Hom.: 0 Cov.: 31 AF XY: 0.00000697 AC XY: 5AN XY: 717680
GnomAD4 genome AF: 0.0000395 AC: 6AN: 151838Hom.: 0 Cov.: 30 AF XY: 0.0000270 AC XY: 2AN XY: 74146
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.-3G>T variant is located in the 5' untranslated region (5’ UTR) of the STXBP1 gene. This variant results from a G to T substitution 3 bases upstream from the first translated codon. This nucleotide position is highly conserved in available vertebrate species. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -
not provided Benign:1
Has not been previously published as pathogenic or benign to our knowledge; Regulatory variants have not been reported in the Human Gene Mutation Database in individuals with STXBP1-related disorders (Stenson et al., 2014) -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at