rs73116571
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_002466.4(MYBL2):c.1365+3G>T variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0055 in 1,582,218 control chromosomes in the GnomAD database, including 26 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: 𝑓 0.0039 ( 3 hom., cov: 32)
Exomes 𝑓: 0.0057 ( 23 hom. )
Consequence
MYBL2
NM_002466.4 splice_donor_region, intron
NM_002466.4 splice_donor_region, intron
Scores
2
Splicing: ADA: 0.03313
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.309
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 -8 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.72).
BS2
?
High AC in GnomAd4 at 587 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYBL2 | NM_002466.4 | c.1365+3G>T | splice_donor_region_variant, intron_variant | ENST00000217026.5 | |||
MYBL2 | NM_001278610.2 | c.1293+3G>T | splice_donor_region_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYBL2 | ENST00000217026.5 | c.1365+3G>T | splice_donor_region_variant, intron_variant | 1 | NM_002466.4 | P1 | |||
MYBL2 | ENST00000396863.8 | c.1293+3G>T | splice_donor_region_variant, intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00386 AC: 587AN: 152206Hom.: 3 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.00375 AC: 885AN: 235982Hom.: 4 AF XY: 0.00372 AC XY: 470AN XY: 126422
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GnomAD4 exome AF: 0.00568 AC: 8121AN: 1429894Hom.: 23 Cov.: 31 AF XY: 0.00548 AC XY: 3862AN XY: 705198
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GnomAD4 genome ? AF: 0.00385 AC: 587AN: 152324Hom.: 3 Cov.: 32 AF XY: 0.00379 AC XY: 282AN XY: 74480
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ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Calibrated prediction
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at