20-37020730-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_002895.5(RBL1):c.2560G>A(p.Val854Ile) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.000116 in 1,560,270 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002895.5 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RBL1 | ENST00000373664.8 | c.2560G>A | p.Val854Ile | missense_variant, splice_region_variant | Exon 18 of 22 | 1 | NM_002895.5 | ENSP00000362768.3 | ||
RBL1 | ENST00000344359.7 | c.2560G>A | p.Val854Ile | missense_variant, splice_region_variant | Exon 18 of 21 | 1 | ENSP00000343646.3 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 151972Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000346 AC: 7AN: 202556Hom.: 0 AF XY: 0.0000459 AC XY: 5AN XY: 108890
GnomAD4 exome AF: 0.000123 AC: 173AN: 1408298Hom.: 0 Cov.: 27 AF XY: 0.000110 AC XY: 77AN XY: 699360
GnomAD4 genome AF: 0.0000526 AC: 8AN: 151972Hom.: 0 Cov.: 31 AF XY: 0.0000404 AC XY: 3AN XY: 74210
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2560G>A (p.V854I) alteration is located in exon 18 (coding exon 18) of the RBL1 gene. This alteration results from a G to A substitution at nucleotide position 2560, causing the valine (V) at amino acid position 854 to be replaced by an isoleucine (I). 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