chr12-57526046-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_052897.4(MBD6):c.1078C>T(p.Arg360Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000748 in 1,614,010 control chromosomes in the GnomAD database, including 15 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_052897.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MBD6 | NM_052897.4 | c.1078C>T | p.Arg360Cys | missense_variant | 6/13 | ENST00000355673.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MBD6 | ENST00000355673.8 | c.1078C>T | p.Arg360Cys | missense_variant | 6/13 | 1 | NM_052897.4 | P1 | |
MBD6 | ENST00000552659.1 | c.365-265C>T | intron_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.00398 AC: 605AN: 152056Hom.: 6 Cov.: 31
GnomAD3 exomes AF: 0.00105 AC: 263AN: 251156Hom.: 4 AF XY: 0.000825 AC XY: 112AN XY: 135776
GnomAD4 exome AF: 0.000412 AC: 602AN: 1461836Hom.: 9 Cov.: 38 AF XY: 0.000364 AC XY: 265AN XY: 727216
GnomAD4 genome AF: 0.00398 AC: 606AN: 152174Hom.: 6 Cov.: 31 AF XY: 0.00343 AC XY: 255AN XY: 74392
ClinVar
Submissions by phenotype
MBD6-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 23, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at