16-30992826-A-G
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_052874.5(STX1B):c.862T>C(p.Leu288=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000412 in 1,457,442 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 Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. L288L) has been classified as Likely benign.
Frequency
Consequence
NM_052874.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STX1B | NM_052874.5 | c.862T>C | p.Leu288= | synonymous_variant | 10/10 | ENST00000215095.11 | |
STX1B | XM_017022893.2 | c.844T>C | p.Leu282= | synonymous_variant | 10/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STX1B | ENST00000215095.11 | c.862T>C | p.Leu288= | synonymous_variant | 10/10 | 1 | NM_052874.5 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD3 exomes AF: 0.0000201 AC: 5AN: 248660Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 134818
GnomAD4 exome AF: 0.00000412 AC: 6AN: 1457442Hom.: 0 Cov.: 31 AF XY: 0.00000414 AC XY: 3AN XY: 725302
GnomAD4 genome ? Cov.: 31
ClinVar
Submissions by phenotype
Generalized epilepsy with febrile seizures plus, type 9 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 23, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at