rs549586410
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_004701.4(CCNB2):c.25G>A(p.Val9Met) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000137 in 1,532,386 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_004701.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCNB2 | ENST00000288207.7 | c.25G>A | p.Val9Met | missense_variant, splice_region_variant | Exon 2 of 9 | 1 | NM_004701.4 | ENSP00000288207.2 | ||
CCNB2 | ENST00000621385.1 | c.25G>A | p.Val9Met | missense_variant, splice_region_variant | Exon 2 of 8 | 1 | ENSP00000480809.1 | |||
CCNB2 | ENST00000559622.5 | c.24+2030G>A | intron_variant | Intron 1 of 5 | 5 | ENSP00000453685.1 | ||||
CCNB2 | ENST00000561077.1 | n.168G>A | splice_region_variant, non_coding_transcript_exon_variant | Exon 2 of 3 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000416 AC: 6AN: 144360Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000281 AC: 6AN: 213566Hom.: 0 AF XY: 0.0000258 AC XY: 3AN XY: 116428
GnomAD4 exome AF: 0.0000108 AC: 15AN: 1387934Hom.: 0 Cov.: 32 AF XY: 0.0000174 AC XY: 12AN XY: 688014
GnomAD4 genome AF: 0.0000415 AC: 6AN: 144452Hom.: 0 Cov.: 32 AF XY: 0.0000573 AC XY: 4AN XY: 69854
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at