chr12-57525894-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_052897.4(MBD6):c.926C>T(p.Thr309Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000676 in 1,612,742 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_052897.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MBD6 | NM_052897.4 | c.926C>T | p.Thr309Met | missense_variant | 6/13 | ENST00000355673.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MBD6 | ENST00000355673.8 | c.926C>T | p.Thr309Met | missense_variant | 6/13 | 1 | NM_052897.4 | P1 | |
MBD6 | ENST00000552659.1 | c.365-417C>T | intron_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000923 AC: 14AN: 151744Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000929 AC: 23AN: 247518Hom.: 0 AF XY: 0.0000892 AC XY: 12AN XY: 134554
GnomAD4 exome AF: 0.0000650 AC: 95AN: 1460998Hom.: 0 Cov.: 38 AF XY: 0.0000633 AC XY: 46AN XY: 726846
GnomAD4 genome AF: 0.0000923 AC: 14AN: 151744Hom.: 0 Cov.: 30 AF XY: 0.000108 AC XY: 8AN XY: 74068
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 17, 2022 | The c.926C>T (p.T309M) alteration is located in exon 6 (coding exon 4) of the MBD6 gene. This alteration results from a C to T substitution at nucleotide position 926, causing the threonine (T) at amino acid position 309 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at