chr16-30992860-C-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_052874.5(STX1B):c.828G>T(p.Val276=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,726 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. V276V) has been classified as Benign.
Frequency
Consequence
NM_052874.5 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STX1B | NM_052874.5 | c.828G>T | p.Val276= | synonymous_variant | 10/10 | ENST00000215095.11 | |
STX1B | XM_017022893.2 | c.810G>T | p.Val270= | synonymous_variant | 10/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STX1B | ENST00000215095.11 | c.828G>T | p.Val276= | synonymous_variant | 10/10 | 1 | NM_052874.5 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461726Hom.: 0 Cov.: 34 AF XY: 0.00000413 AC XY: 3AN XY: 727162
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Generalized epilepsy with febrile seizures plus, type 9 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 03, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at