rs1060503088
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_ModeratePP5_Moderate
The NM_000321.3(RB1):c.1696-12T>G variant causes a splice polypyrimidine tract, 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. Variant has been reported in ClinVar as Pathogenic (★).
Frequency
Genomes: not found (cov: 32)
Consequence
RB1
NM_000321.3 splice_polypyrimidine_tract, intron
NM_000321.3 splice_polypyrimidine_tract, intron
Scores
2
Splicing: ADA: 0.9997
2
Clinical Significance
Conservation
PhyloP100: 1.66
Genes affected
RB1 (HGNC:9884): (RB transcriptional corepressor 1) The protein encoded by this gene is a negative regulator of the cell cycle and was the first tumor suppressor gene found. The encoded protein also stabilizes constitutive heterochromatin to maintain the overall chromatin structure. The active, hypophosphorylated form of the protein binds transcription factor E2F1. Defects in this gene are a cause of childhood cancer retinoblastoma (RB), bladder cancer, and osteogenic sarcoma. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PP3
?
Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF, max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
PP5
?
Variant 13-48452981-T-G is Pathogenic according to our data. Variant chr13-48452981-T-G is described in ClinVar as [Pathogenic]. Clinvar id is 410940.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RB1 | NM_000321.3 | c.1696-12T>G | splice_polypyrimidine_tract_variant, intron_variant | ENST00000267163.6 | |||
RB1 | NM_001407165.1 | c.1696-12T>G | splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RB1 | ENST00000267163.6 | c.1696-12T>G | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_000321.3 | P1 | |||
RB1 | ENST00000643064.1 | c.194+71538T>G | intron_variant | ||||||
RB1 | ENST00000650461.1 | c.1696-12T>G | splice_polypyrimidine_tract_variant, intron_variant | ||||||
RB1 | ENST00000480491.1 | n.395-12T>G | splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome Cov.: 31
GnomAD4 exome
Cov.:
31
GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Retinoblastoma Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Aug 03, 2016 | For these reasons, this variant has been classified as Pathogenic. Experimental studies have reported that this variant creates a cryptic acceptor site in intron 17, which inserts 11 nucleotides of intronic sequence into the transcript, resulting in a frameshift and a premature truncation (PMID: 18181215). This variant has been reported in individuals affected with bilateral retinoblastoma (PMID: 18181215, 21520333, Invitae Database). In one of these individuals, family studies indicate this variant likely was not inherited from either parent (i.e. occurred de novo) (Invitae database). This variant is also known as IVS17-12 T>G in the literature. This variant is not present in population databases (ExAC no frequency). This sequence change falls in intron 17 of the RB1 mRNA. It does not directly change the encoded amino acid sequence of the RB1 protein. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Pathogenic
dbscSNV1_RF
Pathogenic
SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_AG_spliceai
Position offset: 1
DS_AL_spliceai
Position offset: 12
Find out detailed SpliceAI scores and Pangolin per-transcript scores at