9-127690839-T-A
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 3P and 4B. PM2PP2BP4_Strong
The NM_001032221.6(STXBP1):c.1767T>A(p.Asp589Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,770 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001032221.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STXBP1 | NM_001032221.6 | c.1767T>A | p.Asp589Glu | missense_variant | 19/19 | ENST00000373299.5 | |
STXBP1 | NM_003165.6 | c.*81T>A | 3_prime_UTR_variant | 20/20 | ENST00000373302.8 | ||
MIR3911 | NR_037473.1 | upstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STXBP1 | ENST00000373299.5 | c.1767T>A | p.Asp589Glu | missense_variant | 19/19 | 1 | NM_001032221.6 | A1 | |
STXBP1 | ENST00000373302.8 | c.*81T>A | 3_prime_UTR_variant | 20/20 | 1 | NM_003165.6 | P3 | ||
ENST00000624141.1 | n.2A>T | non_coding_transcript_exon_variant | 1/1 | ||||||
MIR3911 | ENST00000577791.1 | upstream_gene_variant |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461770Hom.: 0 Cov.: 30 AF XY: 0.00000413 AC XY: 3AN XY: 727174
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Nov 14, 2019 | Not observed in large population cohorts (Lek et al., 2016); In silico analysis, which includes splice predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at