rs1565309133
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PVS1_ModeratePM2
The NM_145309.6(LRRC51):c.-140+1G>A variant causes a splice donor, intron change. The variant allele was found at a frequency of 0.00000656 in 152,336 control chromosomes in the GnomAD database, with no homozygous occurrence. 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_145309.6 splice_donor, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LRRC51 | NM_145309.6 | c.-140+1G>A | splice_donor_variant, intron_variant | Intron 1 of 5 | ENST00000289488.8 | NP_660352.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LRRC51 | ENST00000289488.8 | c.-140+1G>A | splice_donor_variant, intron_variant | Intron 1 of 5 | 1 | NM_145309.6 | ENSP00000289488.2 | |||
LRTOMT | ENST00000307198.11 | c.-322+1G>A | splice_donor_variant, intron_variant | Intron 1 of 6 | 2 | ENSP00000305742.7 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152218Hom.: 0 Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 314Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 220
GnomAD4 genome AF: 0.00000656 AC: 1AN: 152336Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74486
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.