17-4551871-A-G
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_014520.4(MYBBP1A):c.1023+9T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 1,609,522 control chromosomes in the GnomAD database, including 43,069 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 0.20 ( 3701 hom., cov: 34)
Exomes 𝑓: 0.22 ( 39368 hom. )
Consequence
MYBBP1A
NM_014520.4 intron
NM_014520.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.62
Genes affected
MYBBP1A (HGNC:7546): (MYB binding protein 1a) This gene encodes a nucleolar transcriptional regulator that was first identified by its ability to bind specifically to the Myb proto-oncogene protein. The encoded protein is thought to play a role in many cellular processes including response to nucleolar stress, tumor suppression and synthesis of ribosomal DNA. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Sep 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.529 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYBBP1A | NM_014520.4 | c.1023+9T>C | intron_variant | ENST00000254718.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYBBP1A | ENST00000254718.9 | c.1023+9T>C | intron_variant | 1 | NM_014520.4 | P2 | |||
MYBBP1A | ENST00000573116.5 | c.781+9T>C | intron_variant | 1 | |||||
MYBBP1A | ENST00000381556.6 | c.1023+9T>C | intron_variant | 5 | A2 |
Frequencies
GnomAD3 genomes AF: 0.201 AC: 30639AN: 152078Hom.: 3682 Cov.: 34
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GnomAD3 exomes AF: 0.249 AC: 62146AN: 249092Hom.: 9233 AF XY: 0.247 AC XY: 33393AN XY: 135120
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GnomAD4 exome AF: 0.220 AC: 321075AN: 1457326Hom.: 39368 Cov.: 31 AF XY: 0.222 AC XY: 160706AN XY: 725204
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GnomAD4 genome AF: 0.201 AC: 30666AN: 152196Hom.: 3701 Cov.: 34 AF XY: 0.207 AC XY: 15389AN XY: 74406
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Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
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DANN
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RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at