rs1131690858

Positions:

• chr13-48473390-GGTGA-G

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1_Moderate PM2 PP5_Very_Strong

The NM_000321.3(RB1):​c.2520+3_2520+6del variant causes a splice donor, splice donor region, intron change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 1/1 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: RB1 NM_000321.3 splice_donor, splice_donor_region, intron
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:5
• Conservation: PhyloP100: 8.77

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 12 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) variant, product NOT destroyed by NMD, known LOF gene, truncates exone, which is 0.010764263 fraction of the gene. Cryptic splice site detected, with MaxEntScore 3.6, offset of 0 (no position change), new splice context is: gggGTattt. Cryptic site results in inframe change. If cryptic site found is not functional and variant results in exon loss, it results in frameshift change.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 13-48473390-GGTGA-G is Pathogenic according to our data. Variant chr13-48473390-GGTGA-G is described in ClinVar as [Likely_pathogenic]. Clinvar id is 428676.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RB1	NM_000321.3	c.2520+3_2520+6del		splice_donor_variant, splice_donor_region_variant, intron_variant		ENST00000267163.6	NP_000312.2
RB1	NM_001407165.1	c.2520+3_2520+6del		splice_donor_variant, splice_donor_region_variant, intron_variant			NP_001394094.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RB1	ENST00000267163.6	c.2520+3_2520+6del		splice_donor_variant, splice_donor_region_variant, intron_variant		1	NM_000321.3	ENSP00000267163	P1
RB1	ENST00000643064.1	c.194+91950_194+91953del		intron_variant				ENSP00000496005
RB1	ENST00000650461.1	c.2520+3_2520+6del		splice_donor_variant, splice_donor_region_variant, intron_variant				ENSP00000497193

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:5

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Retinoblastoma Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Genetic Diagnostic Laboratory, University of Pennsylvania School of Medicine	May 20, 2024	Case and Pedigree Information: BILATERAL CASES:4, UNILATERAL CASES:0, TOTAL CASES:4, PEDIGREES:4. ACMG Codes Applied:PM2, PS4SUP -
Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Sep 08, 2023	This sequence change falls in intron 24 of the RB1 gene. It does not directly change the encoded amino acid sequence of the RB1 protein. It affects a nucleotide within the consensus splice site. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individual(s) with retinoblastoma (PMID: 7881418, 8605116, 25754945). In at least one individual the variant was observed to be de novo. This variant is also known as IVS24+3del4. ClinVar contains an entry for this variant (Variation ID: 428676). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic. -

not provided Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

GeneDx

Oct 06, 2023

Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports a deleterious effect on splicing and patient-derived cDNA analysis indicates skipping of exon 24 (Houdayer et al., 2008); This variant is associated with the following publications: (PMID: 8346255, 12541220, 18449911, 34247193, 7881418, 34277001, 8605116, 25754945, 24249257, 37602348) -

Hereditary cancer-predisposing syndrome Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Nov 18, 2021

The c.2520+3_2520+6delGAGT intronic pathogenic mutation, located in intron 24 of the RB1 gene, results from a deletion of 4 nucleotides within intron 24 of the RB1 gene. This pathogenic mutation has been reported in the germline of multiple individuals diagnosed with sporadic or hereditary retinoblastoma (RB) (Ambry internal data; Lohmann DR et al. Hum. Mol. Genet. 1994 Dec;3:2187-93; Liu Z et al. Genes Chromosomes Cancer. 1995 Dec;14:277-84; Sagi M et al. Fam. Cancer. 2015 Sep;14:471-80). This pathogenic mutation has also been detected in the tumor of an individual with unilateral RB (Hogg A et al. Proc. Natl. Acad. Sci. U.S.A. 1993 Aug;90:7351-5). In addition this mutation leads to the skipping of exon 24 (Ambry internal data; Houdayer et al. Hum Mutat. 2008;29(7):975-82). Of note, this alteration is also designated as g.170405del4 and IVS24+3del4 in published literature. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -

Hereditary retinoblastoma Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Genetics and Molecular Pathology, SA Pathology

Jun 26, 2020

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Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.76		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.76		Position offset: 0

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

Publications

LitVar

Other links and lift over

dbSNP: rs1131690858; hg19: chr13-49047526;