13-48349024-G-T

Variant summary

Our verdict is Pathogenic. Variant got 20 ACMG points: 20P and 0B. PVS1 PM2 PP3_Moderate PP5_Very_Strong

The NM_000321.3(RB1):c.607+1G>T variant causes a splice donor 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:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 6.9e-7 (0 hom.)
• Consequence: RB1 NM_000321.3 splice_donor
• Scores: Splicing: ADA: 0.9999
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:6
• Conservation: PhyloP100: 4.00

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]

ACMG classification

Verdict is Pathogenic. Variant got 20 ACMG points.

• PVS1: Splicing variant, LoF is a know mechanism of disease, No cryptic splice site detected. Exon removal results in frameshift change.
• 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 13-48349024-G-T is Pathogenic according to our data. Variant chr13-48349024-G-T is described in ClinVar as [Pathogenic]. Clinvar id is 13093.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RB1	NM_000321.3	c.607+1G>T		splice_donor_variant		ENST00000267163.6
RB1	NM_001407165.1	c.607+1G>T		splice_donor_variant
RB1	NM_001407166.1	c.607+1G>T		splice_donor_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RB1	ENST00000267163.6	c.607+1G>T		splice_donor_variant		1	NM_000321.3	P1
RB1	ENST00000467505.5	c.138-10993G>T		intron_variant, NMD_transcript_variant		1
RB1	ENST00000650461.1	c.607+1G>T		splice_donor_variant
RB1	ENST00000525036.1	n.769+1G>T		splice_donor_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 6.93e-7 AC: 1 AN: 1442952 Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0 AN XY: 717874

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0000195

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:6

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Retinoblastoma Pathogenic:4

Pathogenic, criteria provided, single submitter	clinical testing	St. Jude Molecular Pathology, St. Jude Children's Research Hospital	Sep 26, 2023	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. -
Pathogenic, no assertion criteria provided	literature only	OMIM	Jul 01, 2002	- -
Pathogenic, criteria provided, single submitter	clinical testing	Centre for Mendelian Genomics, University Medical Centre Ljubljana	Mar 14, 2014	- -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Nov 13, 2023	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 disrupted 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 introduces a premature termination codon (PMID: 18000883). The resulting mRNA is expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic. -

not provided Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

GeneDx

Aug 24, 2022

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

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Apr 11, 2022

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. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.63	D
BayesDel_noAF	Uncertain	0.11
Cadd	Pathogenic	34
Dann	Uncertain	0.98
Eigen	Pathogenic	1.0
Eigen_PC	Pathogenic	0.84
FATHMM_MKL	Uncertain	0.90	D
MutationTaster	Benign	1.0	D
GERP RS		4.2

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.94
SpliceAI score (max)		1.0		Details are displayed if max score is > 0.2
DS_DL_spliceai		1.0		Position offset: -1

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs587776789; hg19: chr13-48923160; COSMIC: COSV57294293;