13-48303762-G-C
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 0P and 3B. BP4_ModerateBS2_Supporting
The NM_000321.3(RB1):c.-151G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000654 in 1,223,032 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_000321.3 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RB1 | NM_000321.3 | c.-151G>C | 5_prime_UTR_variant | Exon 1 of 27 | ENST00000267163.6 | NP_000312.2 | ||
RB1 | NM_001407165.1 | c.-151G>C | 5_prime_UTR_variant | Exon 1 of 27 | NP_001394094.1 | |||
RB1 | NM_001407166.1 | c.-151G>C | 5_prime_UTR_variant | Exon 1 of 17 | NP_001394095.1 | |||
RB1 | NM_001407167.1 | c.-151G>C | 5_prime_UTR_variant | Exon 1 of 3 | NP_001394096.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152158Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000560 AC: 6AN: 1070874Hom.: 0 Cov.: 15 AF XY: 0.00 AC XY: 0AN XY: 527936
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152158Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74324
ClinVar
Submissions by phenotype
Retinoblastoma Uncertain:1
This variant occurs in a non-coding region of the RB1 gene. It does not change the encoded amino acid sequence of the RB1 protein. This variant is present in population databases (no rsID available, gnomAD 0.06%). This variant has not been reported in the literature in individuals affected with RB1-related conditions. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at