20-37022736-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PP3_ModerateBS2
The NM_002895.5(RBL1):c.2473G>A(p.Glu825Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000496 in 1,613,888 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002895.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RBL1 | ENST00000373664.8 | c.2473G>A | p.Glu825Lys | missense_variant | Exon 17 of 22 | 1 | NM_002895.5 | ENSP00000362768.3 | ||
RBL1 | ENST00000344359.7 | c.2473G>A | p.Glu825Lys | missense_variant | Exon 17 of 21 | 1 | ENSP00000343646.3 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152210Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251400Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135868
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461678Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 727170
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152210Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74370
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2473G>A (p.E825K) alteration is located in exon 17 (coding exon 17) of the RBL1 gene. This alteration results from a G to A substitution at nucleotide position 2473, causing the glutamic acid (E) at amino acid position 825 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at