rs3092886
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000321.3(RB1):c.1216-29A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00437 in 1,612,740 control chromosomes in the GnomAD database, including 265 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). There are indicators that this mutation may affect the branch point..
Frequency
Consequence
NM_000321.3 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RB1 | NM_000321.3 | c.1216-29A>G | intron_variant | ENST00000267163.6 | |||
LOC112268118 | XR_002957522.2 | n.41-2649T>C | intron_variant, non_coding_transcript_variant | ||||
RB1 | NM_001407165.1 | c.1216-29A>G | intron_variant | ||||
RB1 | NM_001407166.1 | c.1216-29A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RB1 | ENST00000267163.6 | c.1216-29A>G | intron_variant | 1 | NM_000321.3 | P1 | |||
RB1 | ENST00000650461.1 | c.1216-29A>G | intron_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0237 AC: 3613AN: 152156Hom.: 156 Cov.: 32
GnomAD3 exomes AF: 0.00626 AC: 1568AN: 250532Hom.: 55 AF XY: 0.00456 AC XY: 618AN XY: 135496
GnomAD4 exome AF: 0.00235 AC: 3439AN: 1460466Hom.: 110 Cov.: 30 AF XY: 0.00206 AC XY: 1500AN XY: 726586
GnomAD4 genome ? AF: 0.0237 AC: 3616AN: 152274Hom.: 155 Cov.: 32 AF XY: 0.0224 AC XY: 1665AN XY: 74454
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 23, 2018 | This variant is associated with the following publications: (PMID: 16343894, 27884173) - |
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Aug 19, 2015 | - - |
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Jun 15, 2023 | - - |
Retinoblastoma Benign:2
Benign, criteria provided, single submitter | clinical testing | KCCC/NGS Laboratory, Kuwait Cancer Control Center | Jul 07, 2023 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 02, 2024 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Hereditary cancer-predisposing syndrome Benign:1
Benign, criteria provided, single submitter | curation | Sema4, Sema4 | Feb 06, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at