15-59114468-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_004701.4(CCNB2):c.292G>A(p.Val98Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000206 in 1,457,580 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. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_004701.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCNB2 | ENST00000288207.7 | c.292G>A | p.Val98Ile | missense_variant | Exon 4 of 9 | 1 | NM_004701.4 | ENSP00000288207.2 | ||
CCNB2 | ENST00000621385.1 | c.292G>A | p.Val98Ile | missense_variant | Exon 4 of 8 | 1 | ENSP00000480809.1 | |||
CCNB2 | ENST00000559622.5 | c.49G>A | p.Val17Ile | missense_variant | Exon 2 of 6 | 5 | ENSP00000453685.1 | |||
CCNB2 | ENST00000561077.1 | n.541G>A | non_coding_transcript_exon_variant | Exon 3 of 3 | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000121 AC: 3AN: 247744Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 133940
GnomAD4 exome AF: 0.00000206 AC: 3AN: 1457580Hom.: 0 Cov.: 32 AF XY: 0.00000276 AC XY: 2AN XY: 724920
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at