2-148469904-A-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_ModerateBP6_Very_StrongBS2
The NM_001378120.1(MBD5):c.1961A>T(p.Asp654Val) variant causes a missense change. The variant allele was found at a frequency of 0.0000613 in 1,613,958 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D654E) has been classified as Uncertain significance.
Frequency
Consequence
NM_001378120.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MBD5 | NM_001378120.1 | c.1961A>T | p.Asp654Val | missense_variant | 8/14 | ENST00000642680.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MBD5 | ENST00000642680.2 | c.1961A>T | p.Asp654Val | missense_variant | 8/14 | NM_001378120.1 |
Frequencies
GnomAD3 genomes ? AF: 0.000256 AC: 39AN: 152182Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000998 AC: 25AN: 250422Hom.: 0 AF XY: 0.0000370 AC XY: 5AN XY: 135294
GnomAD4 exome AF: 0.0000410 AC: 60AN: 1461658Hom.: 0 Cov.: 33 AF XY: 0.0000371 AC XY: 27AN XY: 727132
GnomAD4 genome ? AF: 0.000256 AC: 39AN: 152300Hom.: 0 Cov.: 32 AF XY: 0.000255 AC XY: 19AN XY: 74484
ClinVar
Submissions by phenotype
Intellectual disability, autosomal dominant 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 28, 2020 | This variant is associated with the following publications: (PMID: 17847001) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at