rs4807122
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001281453.2(MBD3):c.111-1061G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.542 in 152,134 control chromosomes in the GnomAD database, including 24,704 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 0.54 ( 24698 hom., cov: 32)
Exomes 𝑓: 0.39 ( 6 hom. )
Consequence
MBD3
NM_001281453.2 intron
NM_001281453.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.252
Genes affected
MBD3 (HGNC:6918): (methyl-CpG binding domain protein 3) DNA methylation is the major modification of eukaryotic genomes and plays an essential role in mammalian development. This gene belongs to a family of nuclear proteins which are characterized by the presence of a methyl-CpG binding domain (MBD). The encoded protein is a subunit of the NuRD, a multisubunit complex containing nucleosome remodeling and histone deacetylase activities. Unlike the other family members, the encoded protein is not capable of binding to methylated DNA. The protein mediates the association of metastasis-associated protein 2 with the core histone deacetylase complex. Alternative splicing results in multiple transcript variants of this gene. [provided by RefSeq, Jul 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=-0.89).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.811 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MBD3 | NM_001281453.2 | c.111-1061G>A | intron_variant | ENST00000434436.8 | NP_001268382.1 | |||
MBD3 | NM_001281454.2 | c.15-1061G>A | intron_variant | NP_001268383.1 | ||||
MBD3 | XM_047438939.1 | c.111-1061G>A | intron_variant | XP_047294895.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.541 AC: 82268AN: 151952Hom.: 24653 Cov.: 32
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GnomAD4 exome AF: 0.391 AC: 25AN: 64Hom.: 6 Cov.: 0 AF XY: 0.333 AC XY: 16AN XY: 48
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GnomAD4 genome AF: 0.542 AC: 82372AN: 152070Hom.: 24698 Cov.: 32 AF XY: 0.542 AC XY: 40284AN XY: 74338
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ClinVar
Not reported inComputational scores
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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