chr9-35748672-G-A
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_020944.3(GBA2):c.33C>T(p.Thr11Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0472 in 1,586,674 control chromosomes in the GnomAD database, including 2,380 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_020944.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GBA2 | ENST00000378103.7 | c.33C>T | p.Thr11Thr | synonymous_variant | Exon 1 of 17 | 1 | NM_020944.3 | ENSP00000367343.3 | ||
GBA2 | ENST00000378094.4 | c.33C>T | p.Thr11Thr | synonymous_variant | Exon 1 of 17 | 1 | ENSP00000367334.4 | |||
GBA2 | ENST00000489025.1 | n.302C>T | non_coding_transcript_exon_variant | Exon 1 of 3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0662 AC: 10065AN: 152138Hom.: 515 Cov.: 32
GnomAD3 exomes AF: 0.0392 AC: 9188AN: 234474Hom.: 341 AF XY: 0.0372 AC XY: 4701AN XY: 126334
GnomAD4 exome AF: 0.0452 AC: 64813AN: 1434418Hom.: 1864 Cov.: 31 AF XY: 0.0442 AC XY: 31361AN XY: 710304
GnomAD4 genome AF: 0.0662 AC: 10075AN: 152256Hom.: 516 Cov.: 32 AF XY: 0.0640 AC XY: 4763AN XY: 74448
ClinVar
Submissions by phenotype
not specified Benign:2
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. -
Spastic paraplegia Benign:1
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not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at