20-43699999-T-C
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_002466.4(MYBL2):āc.906T>Cā(p.Pro302=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.921 in 1,613,980 control chromosomes in the GnomAD database, including 685,644 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: š 0.93 ( 66189 hom., cov: 31)
Exomes š: 0.92 ( 619455 hom. )
Consequence
MYBL2
NM_002466.4 synonymous
NM_002466.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.17
Genes affected
MYBL2 (HGNC:7548): (MYB proto-oncogene like 2) The protein encoded by this gene, a member of the MYB family of transcription factor genes, is a nuclear protein involved in cell cycle progression. The encoded protein is phosphorylated by cyclin A/cyclin-dependent kinase 2 during the S-phase of the cell cycle and possesses both activator and repressor activities. It has been shown to activate the cell division cycle 2, cyclin D1, and insulin-like growth factor-binding protein 5 genes. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP7
Synonymous conserved (PhyloP=-2.17 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.965 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYBL2 | NM_002466.4 | c.906T>C | p.Pro302= | synonymous_variant | 7/14 | ENST00000217026.5 | |
MYBL2 | NM_001278610.2 | c.834T>C | p.Pro278= | synonymous_variant | 6/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYBL2 | ENST00000217026.5 | c.906T>C | p.Pro302= | synonymous_variant | 7/14 | 1 | NM_002466.4 | P1 | |
MYBL2 | ENST00000396863.8 | c.834T>C | p.Pro278= | synonymous_variant | 6/13 | 2 |
Frequencies
GnomAD3 genomes AF: 0.931 AC: 141675AN: 152102Hom.: 66131 Cov.: 31
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GnomAD3 exomes AF: 0.907 AC: 227843AN: 251226Hom.: 103822 AF XY: 0.913 AC XY: 124051AN XY: 135836
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GnomAD4 exome AF: 0.920 AC: 1344922AN: 1461760Hom.: 619455 Cov.: 76 AF XY: 0.921 AC XY: 670030AN XY: 727188
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GnomAD4 genome AF: 0.931 AC: 141789AN: 152220Hom.: 66189 Cov.: 31 AF XY: 0.932 AC XY: 69344AN XY: 74416
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Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at