rs10494570
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000360851.4(RGL1):c.139-17G>T variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0826 in 1,601,538 control chromosomes in the GnomAD database, including 5,802 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
ENST00000360851.4 splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RGL1 | NM_001297671.3 | c.139-17G>T | splice_polypyrimidine_tract_variant, intron_variant | ENST00000360851.4 | NP_001284600.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RGL1 | ENST00000360851.4 | c.139-17G>T | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001297671.3 | ENSP00000354097 | P1 | |||
RGL1 | ENST00000304685.8 | c.244-17G>T | splice_polypyrimidine_tract_variant, intron_variant | 1 | ENSP00000303192 |
Frequencies
GnomAD3 genomes AF: 0.0901 AC: 13704AN: 152038Hom.: 656 Cov.: 32
GnomAD3 exomes AF: 0.0866 AC: 21287AN: 245772Hom.: 986 AF XY: 0.0865 AC XY: 11489AN XY: 132776
GnomAD4 exome AF: 0.0819 AC: 118641AN: 1449382Hom.: 5148 Cov.: 29 AF XY: 0.0827 AC XY: 59605AN XY: 720578
GnomAD4 genome AF: 0.0901 AC: 13710AN: 152156Hom.: 654 Cov.: 32 AF XY: 0.0905 AC XY: 6734AN XY: 74402
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at