13-48360132-G-T

Variant names:

• chr13-48360132-G-T
• rs1131690848
• NM_000321.3:c.718+5G>T

Variant summary

Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM2 PP3_Strong PP5

The NM_000321.3(RB1):​c.718+5G>T variant causes a splice region, intron change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency: Genomes: not found (cov: 32)
• Consequence: RB1 NM_000321.3 splice_region, intron
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:2 U:1
• Conservation: PhyloP100: 7.18

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 Likely_pathogenic. Variant got 7 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 13-48360132-G-T is Pathogenic according to our data. Variant chr13-48360132-G-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 428666.We mark this variant Likely_pathogenic, oryginal submissions are: {Likely_pathogenic=2, Uncertain_significance=1}.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RB1	NM_000321.3	c.718+5G>T		splice_region_variant, intron_variant	Intron 7 of 26	ENST00000267163.6	NP_000312.2
RB1	NM_001407165.1	c.718+5G>T		splice_region_variant, intron_variant	Intron 7 of 26		NP_001394094.1
RB1	NM_001407166.1	c.718+5G>T		splice_region_variant, intron_variant	Intron 7 of 16		NP_001394095.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RB1	ENST00000267163.6	c.718+5G>T		splice_region_variant, intron_variant	Intron 7 of 26	1	NM_000321.3	ENSP00000267163.4
RB1	ENST00000467505.5	n.*86+5G>T		splice_region_variant, intron_variant	Intron 2 of 2	1		ENSP00000434702.1
RB1	ENST00000650461.1	c.718+5G>T		splice_region_variant, intron_variant	Intron 7 of 26			ENSP00000497193.1
RB1	ENST00000525036.1	n.885G>T		non_coding_transcript_exon_variant	Exon 7 of 7	3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:2 Uncertain:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Retinoblastoma Pathogenic:2

Jul 21, 2021

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. This variant disrupts the c.718+5G nucleotide in the RB1 gene. Other variant(s) that disrupt this nucleotide have been determined to be pathogenic (PMID: 11668642). This suggests that this nucleotide is clinically significant, and that variants that disrupt this position are likely to be disease-causing. Nucleotide substitutions within the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant results in skipping of exon 7, but is expected to preserve the integrity of the reading-frame (Invitae). ClinVar contains an entry for this variant (Variation ID: 428666). This variant has been observed in individual(s) with unilateral retinoblastoma as well as in unaffected related individuals. (Invitae). This variant is not present in population databases (ExAC no frequency). This sequence change falls in intron 7 of the RB1 gene. It does not directly change the encoded amino acid sequence of the RB1 protein. RNA analysis indicates that this variant induces altered splicing and likely results in a shortened protein product. -

May 20, 2024

Genetic Diagnostic Laboratory, University of Pennsylvania School of Medicine

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Case and Pedigree Information: BILATERAL CASES:0, UNILATERAL CASES:1, TOTAL CASES:1, PEDIGREES:1. ACMG Codes Applied:PM2, PP3 -

Hereditary cancer-predisposing syndrome Uncertain:1

Mar 29, 2016

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.718+5G>T intronic variant results from a G to T substitution 5 nucleotides after coding exon 7 in the RB1 gene. This nucleotide position is highly conserved in available vertebrate species. This specific alteration has not been reported in the literature, however, an alteration at the same nucleotide (c.718+5G>A) was identified in a Polish patient with bilateral Retinoblastoma and was shown via RT-PCR to cause exon 7 skipping and an in-frame deletion of 37 amino acids (Jakubowska A, Hum. Mutat. 2001 Nov; 18(5):459). In addition, this alteration is predicted to decrease the efficiency of the native splice donor site by the BDGP and ESEfinder in silico models; however experimental evidence is not currently available. This variant was not reported in population based cohorts in the following databases: Database of Single Nucleotide Polymorphisms (dbSNP), NHLBI Exome Sequencing Project (ESP), and 1000 Genomes Project. In the ESP, this variant was not observed in 6501 samples (13002 alleles) with coverage of 6501 at this position. Since supporting evidence is limited at this time, the clinical significance of this variant remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.21
CADD	Benign	18
DANN	Benign	0.97

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.98
SpliceAI score (max)		0.97		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.97		Position offset: -5

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

Publications

LitVar

Other links and lift over

dbSNP: rs1131690848; hg19: chr13-48934268;