rs4151540
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_001407166.1(RB1):c.*69_*70insAA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.258 in 1,281,506 control chromosomes in the GnomAD database, including 45,161 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.23 ( 4251 hom., cov: 24)
Exomes 𝑓: 0.26 ( 40910 hom. )
Consequence
RB1
NM_001407166.1 3_prime_UTR
NM_001407166.1 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.0210
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant 13-48381523-C-CAA is Benign according to our data. Variant chr13-48381523-C-CAA is described in ClinVar as [Benign]. Clinvar id is 1225861.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RB1 | NM_000321.3 | c.1695+81_1695+82insAA | intron_variant | ENST00000267163.6 | NP_000312.2 | |||
RB1 | NM_001407166.1 | c.*69_*70insAA | 3_prime_UTR_variant | 17/17 | NP_001394095.1 | |||
RB1 | NM_001407165.1 | c.1695+81_1695+82insAA | intron_variant | NP_001394094.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RB1 | ENST00000267163.6 | c.1695+81_1695+82insAA | intron_variant | 1 | NM_000321.3 | ENSP00000267163.4 | ||||
RB1 | ENST00000650461.1 | c.1695+81_1695+82insAA | intron_variant | ENSP00000497193.1 | ||||||
RB1 | ENST00000643064.1 | c.192+81_192+82insAA | intron_variant | ENSP00000496005.1 |
Frequencies
GnomAD3 genomes AF: 0.231 AC: 35087AN: 151906Hom.: 4257 Cov.: 24
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GnomAD4 exome AF: 0.261 AC: 295159AN: 1129482Hom.: 40910 AF XY: 0.261 AC XY: 149955AN XY: 573572
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GnomAD4 genome AF: 0.231 AC: 35082AN: 152024Hom.: 4251 Cov.: 24 AF XY: 0.234 AC XY: 17374AN XY: 74300
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 25, 2018 | - - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at