rs3130018
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001141969.2(DAXX):c.-53+237C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.462 in 305,114 control chromosomes in the GnomAD database, including 35,130 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 0.41 ( 14336 hom., cov: 28)
Exomes 𝑓: 0.51 ( 20794 hom. )
Consequence
DAXX
NM_001141969.2 intron
NM_001141969.2 intron
Scores
2
Splicing: ADA: 0.00004088
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.25
Genes affected
DAXX (HGNC:2681): (death domain associated protein) This gene encodes a multifunctional protein that resides in multiple locations in the nucleus and in the cytoplasm. It interacts with a wide variety of proteins, such as apoptosis antigen Fas, centromere protein C, and transcription factor erythroblastosis virus E26 oncogene homolog 1. In the nucleus, the encoded protein functions as a potent transcription repressor that binds to sumoylated transcription factors. Its repression can be relieved by the sequestration of this protein into promyelocytic leukemia nuclear bodies or nucleoli. This protein also associates with centromeres in G2 phase. In the cytoplasm, the encoded protein may function to regulate apoptosis. The subcellular localization and function of this protein are modulated by post-translational modifications, including sumoylation, phosphorylation and polyubiquitination. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2008]
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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=-0.84).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.589 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DAXX | NM_001141969.2 | c.-53+237C>T | intron_variant | ENST00000374542.10 | |||
LOC124901303 | XR_007059547.1 | upstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DAXX | ENST00000374542.10 | c.-53+237C>T | intron_variant | 1 | NM_001141969.2 | P2 |
Frequencies
GnomAD3 genomes AF: 0.414 AC: 62293AN: 150290Hom.: 14331 Cov.: 28
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GnomAD4 exome AF: 0.507 AC: 78499AN: 154706Hom.: 20794 Cov.: 0 AF XY: 0.522 AC XY: 44001AN XY: 84254
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GnomAD4 genome AF: 0.414 AC: 62335AN: 150408Hom.: 14336 Cov.: 28 AF XY: 0.421 AC XY: 30869AN XY: 73348
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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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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