chr5-168486544-G-A
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 10P and 1B. PVS1PM2BS2_Supporting
The NM_002887.4(RARS1):c.45+1G>A variant causes a splice donor change. The variant allele was found at a frequency of 0.00000356 in 1,404,788 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_002887.4 splice_donor
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RARS1 | NM_002887.4 | c.45+1G>A | splice_donor_variant | ENST00000231572.8 | NP_002878.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RARS1 | ENST00000231572.8 | c.45+1G>A | splice_donor_variant | 1 | NM_002887.4 | ENSP00000231572 | P1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 0.00000356 AC: 5AN: 1404788Hom.: 0 Cov.: 35 AF XY: 0.00000289 AC XY: 2AN XY: 693192
GnomAD4 genome Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at