chr12-57526005-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_052897.4(MBD6):c.1037C>T(p.Pro346Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000372 in 1,613,752 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 Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MBD6 | NM_052897.4 | c.1037C>T | p.Pro346Leu | missense_variant | 6/13 | ENST00000355673.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MBD6 | ENST00000355673.8 | c.1037C>T | p.Pro346Leu | missense_variant | 6/13 | 1 | NM_052897.4 | P1 | |
MBD6 | ENST00000552659.1 | c.365-306C>T | intron_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152024Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250768Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135698
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461728Hom.: 0 Cov.: 38 AF XY: 0.00000550 AC XY: 4AN XY: 727174
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152024Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74274
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 18, 2022 | The c.1037C>T (p.P346L) 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 1037, causing the proline (P) at amino acid position 346 to be replaced by a leucine (L). 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