1-42692759-C-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_004559.5(YBX1):c.231-731C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000092 in 152,158 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000092 ( 0 hom., cov: 33)
Consequence
YBX1
NM_004559.5 intron
NM_004559.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.71
Genes affected
YBX1 (HGNC:8014): (Y-box binding protein 1) This gene encodes a highly conserved cold shock domain protein that has broad nucleic acid binding properties. The encoded protein functions as both a DNA and RNA binding protein and has been implicated in numerous cellular processes including regulation of transcription and translation, pre-mRNA splicing, DNA reparation and mRNA packaging. This protein is also a component of messenger ribonucleoprotein (mRNP) complexes and may have a role in microRNA processing. This protein can be secreted through non-classical pathways and functions as an extracellular mitogen. Aberrant expression of the gene is associated with cancer proliferation in numerous tissues. This gene may be a prognostic marker for poor outcome and drug resistance in certain cancers. Alternate splicing results in multiple transcript variants. Pseudogenes of this gene are found on multiple chromosomes. [provided by RefSeq, Sep 2015]
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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=-0.91).
BS2
High AC in GnomAd4 at 14 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
YBX1 | NM_004559.5 | c.231-731C>T | intron_variant | Intron 2 of 7 | ENST00000321358.12 | NP_004550.2 | ||
YBX1 | XM_047421495.1 | c.231-731C>T | intron_variant | Intron 2 of 5 | XP_047277451.1 | |||
YBX1 | NR_132737.2 | n.231-731C>T | intron_variant | Intron 1 of 6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
YBX1 | ENST00000321358.12 | c.231-731C>T | intron_variant | Intron 2 of 7 | 1 | NM_004559.5 | ENSP00000361626.3 | |||
YBX1 | ENST00000436427.1 | c.378-731C>T | intron_variant | Intron 1 of 6 | 1 | ENSP00000389639.1 | ||||
YBX1 | ENST00000332220.10 | c.231-731C>T | intron_variant | Intron 2 of 4 | 5 | ENSP00000405937.1 | ||||
YBX1 | ENST00000467957.1 | n.312-731C>T | intron_variant | Intron 1 of 4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000921 AC: 14AN: 152040Hom.: 0 Cov.: 33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0000920 AC: 14AN: 152158Hom.: 0 Cov.: 33 AF XY: 0.000108 AC XY: 8AN XY: 74376
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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