rs16994495
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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.*1231A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 152,228 control chromosomes in the GnomAD database, including 1,592 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 0.14 ( 1592 hom., cov: 34)
Exomes 𝑓: 0.14 ( 2 hom. )
Failed GnomAD Quality Control
Consequence
MBD3
NM_001281453.2 3_prime_UTR
NM_001281453.2 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.45
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=-0.97).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.15 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MBD3 | NM_001281453.2 | c.*1231A>G | 3_prime_UTR_variant | 7/7 | ENST00000434436.8 | ||
MBD3 | NM_001281454.2 | c.*1231A>G | 3_prime_UTR_variant | 7/7 | |||
MBD3 | XM_047438939.1 | c.*1407A>G | 3_prime_UTR_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MBD3 | ENST00000434436.8 | c.*1231A>G | 3_prime_UTR_variant | 7/7 | 1 | NM_001281453.2 | P1 | ||
ENST00000624421.1 | upstream_gene_variant |
Frequencies
GnomAD3 genomes ? AF: 0.141 AC: 21516AN: 152110Hom.: 1586 Cov.: 34
GnomAD3 genomes
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.141 AC: 11AN: 78Hom.: 2 Cov.: 0 AF XY: 0.103 AC XY: 6AN XY: 58
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
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GnomAD4 genome ? AF: 0.142 AC: 21547AN: 152228Hom.: 1592 Cov.: 34 AF XY: 0.142 AC XY: 10530AN XY: 74416
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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