chr13-48373493-G-A

Position:

• chr13-48373493-G-A

Variant summary

Our verdict is Pathogenic. Variant got 22 ACMG points: 22P and 0B. PVS1 PM2 PP3_Strong PP5_Very_Strong

The NM_000321.3(RB1):​c.1215+1G>A variant causes a splice donor change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: RB1 NM_000321.3 splice_donor
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:12
• Conservation: PhyloP100: 7.39

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]

LOC112268118 (HGNC:):

ACMG classification

Verdict is Pathogenic. Variant got 22 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) 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 13-48373493-G-A is Pathogenic according to our data. Variant chr13-48373493-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 126832.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr13-48373493-G-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RB1	NM_000321.3	c.1215+1G>A		splice_donor_variant		ENST00000267163.6
LOC112268118	XR_002957522.2	n.121+667C>T		intron_variant, non_coding_transcript_variant
RB1	NM_001407165.1	c.1215+1G>A		splice_donor_variant
RB1	NM_001407166.1	c.1215+1G>A		splice_donor_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RB1	ENST00000267163.6	c.1215+1G>A		splice_donor_variant		1	NM_000321.3	P1
RB1	ENST00000650461.1	c.1215+1G>A		splice_donor_variant

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 1384518 Hom.: 0 Cov.: 25 AF XY: 0.00 AC XY: 0 AN XY: 692604

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: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ExAC AF: 0.00000824 AC: 1

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:12

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Retinoblastoma Pathogenic:9

Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Oct 08, 2023	This sequence change affects a donor splice site in intron 12 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 individuals with retinoblastoma (PMID: 2601691, 12541220, 16463005, 26396485, 27582626). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 126832). Studies have shown that disruption of this splice site results in skipping of exon 12 and introduces a premature termination codon (PMID: 2601691). The resulting mRNA is expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	research	Department of Pediatrics, Memorial Sloan Kettering Cancer Center	Dec 15, 2020	- -
Pathogenic, no assertion criteria provided	clinical testing	Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan	Oct 16, 2019	- -
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:20, UNILATERAL CASES:3, TOTAL CASES:23, PEDIGREES:22. ACMG Codes Applied:PVS1, PM2, PS4S -
Pathogenic, criteria provided, single submitter	research	Genetics Program, Instituto Nacional de Cancer	Aug 20, 2020	- -
Pathogenic, criteria provided, single submitter	clinical testing	St. Jude Molecular Pathology, St. Jude Children's Research Hospital	Feb 02, 2023	The RB1 c.1215+1G>A intronic change results in a G to A substitution at the +1 position of intron 12 of the RB1 gene. This variant results in skipping of exon 12 resulting in nonsense-mediated decay or an abnormal protein product (PVS1). This variant has been identified in individuals with a personal and/or family history of retinoblastoma (PMID: 2601691, 12541220, 29489754, 29568217, 33456302, 34277001, internal data) and osteosarcoma (PMID: 34308366). 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, criteria provided, single submitter	clinical testing	Genetics and Molecular Pathology, SA Pathology	Jun 20, 2022	- -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Dec 03, 2021	Variant summary: RB1 c.1215+1G>A is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Several computational tools predict a significant impact on normal splicing: Three predict the variant abolishes a 5` splicing donor site. At least one publication reports experimental evidence that this variant affects mRNA splicing and results in exon 12 deletion (Dunn_1989). The variant was absent in 249940 control chromosomes (gnomAD). c.1215+1G>A has been reported in the literature in multiple individuals affected with Retinoblastoma (Dunn_1989, Richter_2002, Chai_2021). These data indicate that the variant is very likely to be associated with disease. Six ClinVar submitters (evaluation after 2014) cite the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -
Pathogenic, no assertion criteria provided	literature only	OMIM	Nov 01, 1989	- -

Malignant tumor of urinary bladder Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Baylor Genetics

Oct 26, 2023

- -

Hereditary cancer-predisposing syndrome Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Aug 03, 2023

The c.1215+1G>A intronic pathogenic mutation results from a G to A substitution one nucleotide after coding exon 12 of the RB1 gene. This alteration has been reported as a germline mutation in multiple families affected with bilateral and/or unilateral retinoblastoma (Richter S et al. Am. J. Hum. Genet. 2003 Feb;72(2):253-69; Kiran V et al. Hum. Mutat. 2003 Oct;22(4):339; Houdayer C et al. Hum. Mutat. 2004 Feb;23(2):193-202; Alonso J et al. Hum. Mutat. 2005 Jan;25(1):99; Sivakumaran T et al. Hum. Mutat. 2005 Apr;25(4):396-409; Nichols K et al. Hum. Mutat. 2005 Jun;25(6):566-74; Taylor M et al. Hum. Mutat. 2007 Mar;28(3):284-93; Abouzeid H et al. Mol. Vis. 2007 Sep;13:1740-5). Analysis of RNA from an individual with bilateral retinoblastoma carrying c.1215+1G>A demonstrated that this mutation results in the skipping of coding exon 12, leading to a frameshift and a predicted alternate stop codon (Zhang K et al. Hum. Mutat. 2008 Apr;29(4):475-84). This nucleotide position is highly conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice donor site. Of note, this alteration is also designated as c.1353+1G>A, IVS12+1G>A and g.70330G>A in published literature. 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

Pathogenic, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Oct 31, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.63	D
BayesDel_noAF	Pathogenic	0.35
CADD	Pathogenic	32
DANN	Uncertain	0.99
Eigen	Pathogenic	1.1
Eigen_PC	Pathogenic	0.98
FATHMM_MKL	Uncertain	0.96	D
MutationTaster	Benign	1.0	D
GERP RS		5.4
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.94
SpliceAI score (max)		0.98		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.98		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: rs587776783; hg19: chr13-48947629; COSMIC: COSV57294939;