3-121381436-G-A
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1
The NM_001308330.2(STXBP5L):c.2491G>A(p.Val831Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0972 in 1,605,206 control chromosomes in the GnomAD database, including 8,433 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_001308330.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
STXBP5L | NM_001308330.2 | c.2491G>A | p.Val831Ile | missense_variant | Exon 22 of 27 | ENST00000471454.6 | NP_001295259.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0793 AC: 12043AN: 151816Hom.: 600 Cov.: 32
GnomAD3 exomes AF: 0.0973 AC: 23355AN: 240050Hom.: 1442 AF XY: 0.0934 AC XY: 12192AN XY: 130474
GnomAD4 exome AF: 0.0991 AC: 143966AN: 1453272Hom.: 7832 Cov.: 34 AF XY: 0.0970 AC XY: 70149AN XY: 723000
GnomAD4 genome AF: 0.0793 AC: 12047AN: 151934Hom.: 601 Cov.: 32 AF XY: 0.0789 AC XY: 5853AN XY: 74214
ClinVar
Submissions by phenotype
STXBP5L-related disorder Benign:1
This variant is classified as 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