chr9-35737345-G-A
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PVS1_StrongPM2PP5_Moderate
The NM_020944.3(GBA2):c.2608C>T(p.Arg870Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000805 in 1,614,002 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. R870R) has been classified as Likely benign.
Frequency
Consequence
NM_020944.3 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GBA2 | NM_020944.3 | c.2608C>T | p.Arg870Ter | stop_gained | 17/17 | ENST00000378103.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GBA2 | ENST00000378103.7 | c.2608C>T | p.Arg870Ter | stop_gained | 17/17 | 1 | NM_020944.3 | P1 | |
GBA2 | ENST00000378094.4 | c.*131C>T | 3_prime_UTR_variant | 17/17 | 1 | ||||
GBA2 | ENST00000378088.1 | c.*292C>T | 3_prime_UTR_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152260Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250504Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135550
GnomAD4 exome AF: 0.00000753 AC: 11AN: 1461742Hom.: 0 Cov.: 33 AF XY: 0.00000550 AC XY: 4AN XY: 727168
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152260Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74388
ClinVar
Submissions by phenotype
Hereditary spastic paraplegia 46 Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Mar 08, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at