13-48380051-A-T
Variant summary
Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PVS1PM2PP3_Strong
The NM_000321.3(RB1):c.1390-2A>T variant causes a splice acceptor change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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_000321.3 splice_acceptor
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RB1 | NM_000321.3 | c.1390-2A>T | splice_acceptor_variant | ENST00000267163.6 | |||
RB1 | NM_001407165.1 | c.1390-2A>T | splice_acceptor_variant | ||||
RB1 | NM_001407166.1 | c.1390-2A>T | splice_acceptor_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RB1 | ENST00000267163.6 | c.1390-2A>T | splice_acceptor_variant | 1 | NM_000321.3 | P1 | |||
RB1 | ENST00000650461.1 | c.1390-2A>T | splice_acceptor_variant |
Frequencies
GnomAD3 genomes Cov.: 30
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000535 AC: 6AN: 1122084Hom.: 0 Cov.: 21 AF XY: 0.00000536 AC XY: 3AN XY: 559704
GnomAD4 genome Cov.: 30
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.