NM_052874.5:c.609G>A
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2
The NM_052874.5(STX1B):c.609G>A(p.Lys203Lys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000281 in 1,614,120 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_052874.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
STX1B | ENST00000215095.11 | c.609G>A | p.Lys203Lys | synonymous_variant | Exon 8 of 10 | 1 | NM_052874.5 | ENSP00000215095.5 | ||
STX1B | ENST00000565419.2 | c.609G>A | p.Lys203Lys | synonymous_variant | Exon 8 of 9 | 2 | ENSP00000455899.1 |
Frequencies
GnomAD3 genomes AF: 0.00162 AC: 247AN: 152168Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000410 AC: 103AN: 251418Hom.: 0 AF XY: 0.000324 AC XY: 44AN XY: 135878
GnomAD4 exome AF: 0.000142 AC: 207AN: 1461836Hom.: 0 Cov.: 34 AF XY: 0.000118 AC XY: 86AN XY: 727218
GnomAD4 genome AF: 0.00162 AC: 247AN: 152284Hom.: 1 Cov.: 32 AF XY: 0.00161 AC XY: 120AN XY: 74462
ClinVar
Submissions by phenotype
Generalized epilepsy with febrile seizures plus, type 9 Benign:2
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Inborn genetic diseases Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
not provided Benign:1
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STX1B-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