rs28584995
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_020944.3(GBA2):c.786+6G>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00131 in 1,550,700 control chromosomes in the GnomAD database, including 32 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
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GBA2 | ENST00000378103.7 | c.786+6G>C | splice_region_variant, intron_variant | Intron 4 of 16 | 1 | NM_020944.3 | ENSP00000367343.3 | |||
GBA2 | ENST00000378094.4 | c.786+6G>C | splice_region_variant, intron_variant | Intron 4 of 16 | 1 | ENSP00000367334.4 | ||||
GBA2 | ENST00000467252.5 | n.358+6G>C | splice_region_variant, intron_variant | Intron 1 of 12 | 1 | |||||
GBA2 | ENST00000485259.1 | n.371G>C | non_coding_transcript_exon_variant | Exon 3 of 3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00679 AC: 1032AN: 152024Hom.: 15 Cov.: 32
GnomAD3 exomes AF: 0.00181 AC: 454AN: 251316Hom.: 3 AF XY: 0.00132 AC XY: 179AN XY: 135840
GnomAD4 exome AF: 0.000713 AC: 997AN: 1398558Hom.: 17 Cov.: 25 AF XY: 0.000616 AC XY: 431AN XY: 699364
GnomAD4 genome AF: 0.00680 AC: 1035AN: 152142Hom.: 15 Cov.: 32 AF XY: 0.00649 AC XY: 483AN XY: 74390
ClinVar
Submissions by phenotype
Spastic paraplegia Benign:1
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not provided Benign:1
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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at