rs4807934
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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.111-1004C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.479 in 152,134 control chromosomes in the GnomAD database, including 18,464 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 0.48 ( 18461 hom., cov: 32)
Exomes 𝑓: 0.26 ( 3 hom. )
Consequence
MBD3
NM_001281453.2 intron
NM_001281453.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -3.15
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=-0.93).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.633 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MBD3 | NM_001281453.2 | c.111-1004C>T | intron_variant | ENST00000434436.8 | |||
MBD3 | NM_001281454.2 | c.15-1004C>T | intron_variant | ||||
MBD3 | XM_047438939.1 | c.111-1004C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MBD3 | ENST00000434436.8 | c.111-1004C>T | intron_variant | 1 | NM_001281453.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.479 AC: 72829AN: 151966Hom.: 18441 Cov.: 32
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GnomAD4 exome AF: 0.260 AC: 13AN: 50Hom.: 3 Cov.: 0 AF XY: 0.225 AC XY: 9AN XY: 40
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GnomAD4 genome ? AF: 0.479 AC: 72895AN: 152084Hom.: 18461 Cov.: 32 AF XY: 0.476 AC XY: 35412AN XY: 74340
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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