chr3-32997063-T-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_000404.4(GLB1):c.2016A>T(p.Ser672=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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. S672S) has been classified as Likely benign.
Frequency
Consequence
NM_000404.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GLB1 | NM_000404.4 | c.2016A>T | p.Ser672= | synonymous_variant | 16/16 | ENST00000307363.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GLB1 | ENST00000307363.10 | c.2016A>T | p.Ser672= | synonymous_variant | 16/16 | 1 | NM_000404.4 | P2 | |
GLB1 | ENST00000307377.12 | c.1623A>T | p.Ser541= | synonymous_variant | 13/13 | 1 | |||
GLB1 | ENST00000399402.7 | c.1926A>T | p.Ser642= | synonymous_variant | 16/16 | 2 | A2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 31
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
GM1 gangliosidosis;C0086652:Mucopolysaccharidosis, MPS-IV-B Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 10, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.