rs2240401
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002047.4(GARS1):c.2095-6C>G variant causes a splice region, intron 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. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_002047.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GARS1 | NM_002047.4 | c.2095-6C>G | splice_region_variant, intron_variant | ENST00000389266.8 | NP_002038.2 | |||
GARS1 | NM_001316772.1 | c.1933-6C>G | splice_region_variant, intron_variant | NP_001303701.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GARS1 | ENST00000389266.8 | c.2095-6C>G | splice_region_variant, intron_variant | 1 | NM_002047.4 | ENSP00000373918.3 | ||||
GARS1 | ENST00000675651.1 | c.2113-6C>G | splice_region_variant, intron_variant | ENSP00000502513.1 | ||||||
GARS1 | ENST00000675810.1 | c.1993-6C>G | splice_region_variant, intron_variant | ENSP00000502743.1 | ||||||
GARS1 | ENST00000675693.1 | c.1927-6C>G | splice_region_variant, intron_variant | ENSP00000502174.1 | ||||||
GARS1 | ENST00000675051.1 | c.1894-6C>G | splice_region_variant, intron_variant | ENSP00000502296.1 | ||||||
GARS1 | ENST00000674815.1 | c.1726-6C>G | splice_region_variant, intron_variant | ENSP00000502799.1 | ||||||
GARS1 | ENST00000674851.1 | c.1726-6C>G | splice_region_variant, intron_variant | ENSP00000502451.1 | ||||||
GARS1 | ENST00000444666.6 | n.*516-6C>G | splice_region_variant, intron_variant | 3 | ENSP00000415447.2 | |||||
GARS1 | ENST00000674616.1 | n.*1809-6C>G | splice_region_variant, intron_variant | ENSP00000502408.1 | ||||||
GARS1 | ENST00000674643.1 | n.*1900-6C>G | splice_region_variant, intron_variant | ENSP00000501636.1 | ||||||
GARS1 | ENST00000674737.1 | n.*1433-6C>G | splice_region_variant, intron_variant | ENSP00000502464.1 | ||||||
GARS1 | ENST00000674807.1 | n.*368-6C>G | splice_region_variant, intron_variant | ENSP00000502814.1 | ||||||
GARS1 | ENST00000675529.1 | n.*1965-6C>G | splice_region_variant, intron_variant | ENSP00000501655.1 | ||||||
GARS1 | ENST00000675859.1 | n.*274-6C>G | splice_region_variant, intron_variant | ENSP00000502033.1 | ||||||
GARS1 | ENST00000676088.1 | n.*2037-6C>G | splice_region_variant, intron_variant | ENSP00000501884.1 | ||||||
GARS1 | ENST00000676140.1 | n.*1040-6C>G | splice_region_variant, intron_variant | ENSP00000502571.1 | ||||||
GARS1 | ENST00000676164.1 | n.*1546-6C>G | splice_region_variant, intron_variant | ENSP00000501986.1 | ||||||
GARS1 | ENST00000676210.1 | n.*1384-6C>G | splice_region_variant, intron_variant | ENSP00000502373.1 | ||||||
GARS1 | ENST00000676259.1 | n.*1527-6C>G | splice_region_variant, intron_variant | ENSP00000501980.1 | ||||||
GARS1 | ENST00000676403.1 | n.*180-6C>G | splice_region_variant, intron_variant | ENSP00000502681.1 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 151836Hom.: 0 Cov.: 30 FAILED QC
GnomAD4 exome Cov.: 42
GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 151836Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 74118
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at