rs758083465
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_014520.4(MYBBP1A):c.139C>T(p.Gln47Ter) variant causes a stop gained change. The variant allele was found at a frequency of 0.00000311 in 1,607,838 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000027 ( 0 hom. )
Consequence
MYBBP1A
NM_014520.4 stop_gained
NM_014520.4 stop_gained
Scores
4
2
1
Clinical Significance
Conservation
PhyloP100: 4.63
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 Uncertain_significance. Variant got 2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYBBP1A | NM_014520.4 | c.139C>T | p.Gln47Ter | stop_gained | 1/26 | ENST00000254718.9 | |
MYBBP1A | NM_001105538.2 | c.139C>T | p.Gln47Ter | stop_gained | 1/27 | ||
MYBBP1A | XM_024450536.2 | c.139C>T | p.Gln47Ter | stop_gained | 1/25 | ||
MYBBP1A | XM_047435119.1 | c.139C>T | p.Gln47Ter | stop_gained | 1/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYBBP1A | ENST00000254718.9 | c.139C>T | p.Gln47Ter | stop_gained | 1/26 | 1 | NM_014520.4 | P2 | |
MYBBP1A | ENST00000381556.6 | c.139C>T | p.Gln47Ter | stop_gained | 1/27 | 5 | A2 | ||
MYBBP1A | ENST00000570986.1 | n.173C>T | non_coding_transcript_exon_variant | 1/6 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152252Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.00000840 AC: 2AN: 238074Hom.: 0 AF XY: 0.0000154 AC XY: 2AN XY: 129536
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GnomAD4 exome AF: 0.00000275 AC: 4AN: 1455586Hom.: 0 Cov.: 32 AF XY: 0.00000415 AC XY: 3AN XY: 723642
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GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152252Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74386
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Autism Uncertain:1
Uncertain significance, no assertion criteria provided | research | Lyon Laboratory, Cold Spring Harbor Laboratory | Jul 05, 2015 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Uncertain
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Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Uncertain
D
MutationTaster
Benign
A;A
Vest4
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at