rs73438754
Variant summary
Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_020944.3(GBA2):c.1795+7G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00793 in 1,610,666 control chromosomes in the GnomAD database, including 431 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_020944.3 splice_region, intron
Scores
Clinical Significance
Conservation
Publications
- hereditary spastic paraplegia 46Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae), G2P
- autosomal recessive cerebellar ataxia with late-onset spasticityInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Our verdict: Benign. The variant received -20 ACMG points.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_020944.3. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| GBA2 | NM_020944.3 | MANE Select | c.1795+7G>A | splice_region intron | N/A | NP_065995.1 | |||
| GBA2 | NM_001330660.2 | c.1795+7G>A | splice_region intron | N/A | NP_001317589.1 |
Ensembl Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| GBA2 | ENST00000378103.7 | TSL:1 MANE Select | c.1795+7G>A | splice_region intron | N/A | ENSP00000367343.3 | |||
| GBA2 | ENST00000378094.4 | TSL:1 | c.1795+7G>A | splice_region intron | N/A | ENSP00000367334.4 | |||
| GBA2 | ENST00000467252.5 | TSL:1 | n.1367+7G>A | splice_region intron | N/A |
Frequencies
GnomAD3 genomes AF: 0.0312 AC: 4737AN: 152062Hom.: 214 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.00940 AC: 2347AN: 249766 AF XY: 0.00705 show subpopulations
GnomAD4 exome AF: 0.00550 AC: 8020AN: 1458486Hom.: 217 Cov.: 31 AF XY: 0.00487 AC XY: 3534AN XY: 725554 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.0312 AC: 4754AN: 152180Hom.: 214 Cov.: 32 AF XY: 0.0300 AC XY: 2231AN XY: 74408 show subpopulations
Age Distribution
ClinVar
ClinVar submissions as Germline
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at