chr15-59114866-G-A
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_004701.4(CCNB2):c.587G>A(p.Arg196Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000186 in 1,612,512 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_004701.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCNB2 | ENST00000288207.7 | c.587G>A | p.Arg196Gln | missense_variant | Exon 5 of 9 | 1 | NM_004701.4 | ENSP00000288207.2 | ||
CCNB2 | ENST00000621385.1 | c.587G>A | p.Arg196Gln | missense_variant | Exon 5 of 8 | 1 | ENSP00000480809.1 | |||
CCNB2 | ENST00000559622.5 | c.344G>A | p.Arg115Gln | missense_variant | Exon 3 of 6 | 5 | ENSP00000453685.1 |
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152212Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 250808Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135558
GnomAD4 exome AF: 0.0000171 AC: 25AN: 1460300Hom.: 0 Cov.: 32 AF XY: 0.0000165 AC XY: 12AN XY: 726234
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152212Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74370
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.587G>A (p.R196Q) alteration is located in exon 5 (coding exon 5) of the CCNB2 gene. This alteration results from a G to A substitution at nucleotide position 587, causing the arginine (R) at amino acid position 196 to be replaced by a glutamine (Q). 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