12-57525632-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.664C>T(p.Leu222Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000753 in 1,461,686 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MBD6 | NM_052897.4 | c.664C>T | p.Leu222Phe | missense_variant | Exon 6 of 13 | ENST00000355673.8 | NP_443129.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MBD6 | ENST00000355673.8 | c.664C>T | p.Leu222Phe | missense_variant | Exon 6 of 13 | 1 | NM_052897.4 | ENSP00000347896.3 | ||
MBD6 | ENST00000552659.1 | c.364+517C>T | intron_variant | Intron 3 of 4 | 3 | ENSP00000446834.1 | ||||
MBD6 | ENST00000548887.5 | c.*218C>T | downstream_gene_variant | 4 | ENSP00000448070.1 | |||||
MBD6 | ENST00000549623.1 | c.*177C>T | downstream_gene_variant | 4 | ENSP00000446481.1 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.00000797 AC: 2AN: 250912Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135652
GnomAD4 exome AF: 0.00000753 AC: 11AN: 1461686Hom.: 0 Cov.: 35 AF XY: 0.00000688 AC XY: 5AN XY: 727164
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.664C>T (p.L222F) 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 664, causing the leucine (L) at amino acid position 222 to be replaced by a phenylalanine (F). 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