NM_004701.4:c.53C>A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004701.4(CCNB2):c.53C>A(p.Thr18Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000679 in 147,214 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_004701.4 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 |
---|---|---|---|---|---|---|---|---|---|---|
CCNB2 | ENST00000288207.7 | c.53C>A | p.Thr18Lys | missense_variant | Exon 2 of 9 | 1 | NM_004701.4 | ENSP00000288207.2 | ||
CCNB2 | ENST00000621385.1 | c.53C>A | p.Thr18Lys | missense_variant | Exon 2 of 8 | 1 | ENSP00000480809.1 | |||
CCNB2 | ENST00000559622.5 | c.24+2058C>A | intron_variant | Intron 1 of 5 | 5 | ENSP00000453685.1 | ||||
CCNB2 | ENST00000561077.1 | n.196C>A | non_coding_transcript_exon_variant | Exon 2 of 3 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000679 AC: 1AN: 147214Hom.: 0 Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1453456Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 723160
GnomAD4 genome AF: 0.00000679 AC: 1AN: 147214Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 71250
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at