15-59114592-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_004701.4(CCNB2):āc.416A>Gā(p.Tyr139Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000725 in 1,599,066 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_004701.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCNB2 | ENST00000288207.7 | c.416A>G | p.Tyr139Cys | missense_variant | Exon 4 of 9 | 1 | NM_004701.4 | ENSP00000288207.2 | ||
CCNB2 | ENST00000621385.1 | c.416A>G | p.Tyr139Cys | missense_variant | Exon 4 of 8 | 1 | ENSP00000480809.1 | |||
CCNB2 | ENST00000559622.5 | c.173A>G | p.Tyr58Cys | missense_variant | Exon 2 of 6 | 5 | ENSP00000453685.1 | |||
CCNB2 | ENST00000561077.1 | n.665A>G | non_coding_transcript_exon_variant | Exon 3 of 3 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000302 AC: 46AN: 152210Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000119 AC: 29AN: 242858Hom.: 0 AF XY: 0.0000838 AC XY: 11AN XY: 131314
GnomAD4 exome AF: 0.0000484 AC: 70AN: 1446738Hom.: 0 Cov.: 32 AF XY: 0.0000474 AC XY: 34AN XY: 717634
GnomAD4 genome AF: 0.000302 AC: 46AN: 152328Hom.: 0 Cov.: 32 AF XY: 0.000322 AC XY: 24AN XY: 74486
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.416A>G (p.Y139C) alteration is located in exon 4 (coding exon 4) of the CCNB2 gene. This alteration results from a A to G substitution at nucleotide position 416, causing the tyrosine (Y) at amino acid position 139 to be replaced by a cysteine (C). 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