chr13-48349024-G-T
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_000321.3(RB1):c.607+1G>T variant causes a splice donor, intron change. The variant allele was found at a frequency of 0.000000693 in 1,442,952 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. Variant has been reported in ClinVar as Pathogenic (★★).
Frequency
Consequence
NM_000321.3 splice_donor, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Pathogenic. Variant got 18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RB1 | NM_000321.3 | c.607+1G>T | splice_donor_variant, intron_variant | Intron 6 of 26 | ENST00000267163.6 | NP_000312.2 | ||
RB1 | NM_001407165.1 | c.607+1G>T | splice_donor_variant, intron_variant | Intron 6 of 26 | NP_001394094.1 | |||
RB1 | NM_001407166.1 | c.607+1G>T | splice_donor_variant, intron_variant | Intron 6 of 16 | NP_001394095.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RB1 | ENST00000267163.6 | c.607+1G>T | splice_donor_variant, intron_variant | Intron 6 of 26 | 1 | NM_000321.3 | ENSP00000267163.4 | |||
RB1 | ENST00000467505.5 | n.138-10993G>T | intron_variant | Intron 1 of 2 | 1 | ENSP00000434702.1 | ||||
RB1 | ENST00000650461.1 | c.607+1G>T | splice_donor_variant, intron_variant | Intron 6 of 26 | ENSP00000497193.1 | |||||
RB1 | ENST00000525036.1 | n.769+1G>T | splice_donor_variant, intron_variant | Intron 6 of 6 | 3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.93e-7 AC: 1AN: 1442952Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 717874
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Retinoblastoma Pathogenic:5
- -
The RB1 c.607+1G>T intronic change results in a G to T substitution at the +1 position of intron 6 of the RB1 gene. This variant results in skipping of exon 6 resulting in a premature termination codon and nonsense-mediated decay (PMID: 12016586, 18000883). This variant has been identified in individuals with a personal and/or family history of retinoblastoma (PMID: 8651278, 12016586, 17096365, 28575107, internal data) and osteosarcoma (internal data). Interestingly, there are several reported carriers of this variant who did not develop retinoblastoma. It is thought to be associated with differential penetrance based on the sex of the transmitted parent, where paternally inherited alleles show increased penetrance (PMID: 12016586, 17096365). This variant is absent in gnomAD v2.1.1 (https://gnomad.broadinstitute.org/). In summary, this variant meets criteria to be classified as pathogenic. -
- -
Case and Pedigree Information: BILATERAL CASES:2, UNILATERAL CASES:4, TOTAL CASES:6, PEDIGREES:6. ACMG Codes Applied:PVS1, PM2, PS4SUP -
This sequence change affects a donor splice site in intron 6 of the RB1 gene. RNA analysis indicates that disruption of this splice site induces altered splicing and may result in an absent or altered protein product. This variant is not present in population databases (gnomAD no frequency). Disruption of this splice site has been observed in individual(s) with retinoblastoma (PMID: 8651278, 12016586, 16269091, 17096365, 26925970, 28575107). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 13093). Studies have shown that disruption of this splice site results in skipping of exon 6, and produces a non-functional protein and/or introduces a premature termination codon (PMID: 18000883). For these reasons, this variant has been classified as Pathogenic. -
not provided Pathogenic:1
Canonical splice site variant demonstrated to cause skipping of exon 6 and a premature stop codon in exon 7, resulting in a null allele in a gene for which loss-of-function is a known mechanism of disease (Klutz et al., 2002; Gamez-Pozo et al., 2007); Analysis of multiple families showed increased penetrance when c.607+1G>T was paternally inherited (71% compared to 9% when maternally inherited), suggesting this variant is associated with a parent-of-origin effect (Klutz et al., 2002; Taylor et al., 2007; Buiting et al., 2010); Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 8651278, 24814393, 26925970, 21654082, 25754945, 16269091, 18000883, 14722923, 12541220, 10660960, 11317357, 23820649, 10023315, 25525159, 28575107, 17096365, 20551090, 12016586, 33670346, 34680218) -
Hereditary cancer-predisposing syndrome Pathogenic:1
The c.607+1G>T intronic pathogenic mutation results from a G to T substitution one nucleotide after coding exon 6 of the RB1 gene. This mutation has been reported in multiple individuals/families with retinoblastoma (Ambry internal data; Lohmann DR et al. Am. J. Hum. Genet. 1996 May;58:940-9; Tomar S et al. PLoS ONE. 2017 Jun;12:e0178776; Taylor M et al. Hum. Mutat. 2007 Mar;28:284-93; Klutz M et al. Am. J. Hum. Genet. 2002 Jul;71:174-9). RNA analyses from affected individuals have shown that this alteration leads to skipping of exon 6 (Ambry internal data; Gámez-Pozo A et al. Hum. Mutat. 2007 Dec;28:1245; Klutz M et al. Am. J. Hum. Genet. 2002 Jul;71:174-9). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). In addition to the clinical data presented in the literature, alterations that disrupt the canonical splice site are expected to cause aberrant splicing, resulting in an abnormal protein or a transcript that is subject to nonsense-mediated mRNA decay. As such, this alteration is classified as a disease-causing mutation. -
Malignant tumor of urinary bladder;C0035335:Retinoblastoma;C0149925:Small cell lung carcinoma;C0585442:Bone osteosarcoma Pathogenic:1
PVS1+PM2_Supporting+PS4_Supporting+PP4 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at