rs4533
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_000100.4(CSTB):c.15G>A(p.Ala5=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000167 in 1,375,824 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. A5A) has been classified as Likely benign.
Frequency
Consequence
NM_000100.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CSTB | NM_000100.4 | c.15G>A | p.Ala5= | synonymous_variant | 1/3 | ENST00000291568.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CSTB | ENST00000291568.7 | c.15G>A | p.Ala5= | synonymous_variant | 1/3 | 1 | NM_000100.4 | P1 | |
CSTB | ENST00000640406.1 | c.15G>A | p.Ala5= | synonymous_variant | 1/2 | 2 | |||
CSTB | ENST00000675996.1 | n.76G>A | non_coding_transcript_exon_variant | 1/3 | |||||
CSTB | ENST00000639959.1 | upstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000801 AC: 1AN: 124806Hom.: 0 AF XY: 0.0000147 AC XY: 1AN XY: 67982
GnomAD4 exome AF: 0.0000167 AC: 23AN: 1375824Hom.: 0 Cov.: 31 AF XY: 0.00000884 AC XY: 6AN XY: 678734
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Progressive myoclonic epilepsy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 24, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at