rs201649831
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001378120.1(MBD5):c.2520C>T(p.Gly840Gly) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000368 in 1,603,438 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001378120.1 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MBD5 | NM_001378120.1 | c.2520C>T | p.Gly840Gly | splice_region_variant, synonymous_variant | 9/14 | ENST00000642680.2 | NP_001365049.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MBD5 | ENST00000642680.2 | c.2520C>T | p.Gly840Gly | splice_region_variant, synonymous_variant | 9/14 | NM_001378120.1 | ENSP00000493871.2 |
Frequencies
GnomAD3 genomes AF: 0.00000675 AC: 1AN: 148256Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000813 AC: 2AN: 245890Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 133192
GnomAD4 exome AF: 0.0000399 AC: 58AN: 1455182Hom.: 0 Cov.: 34 AF XY: 0.0000345 AC XY: 25AN XY: 724068
GnomAD4 genome AF: 0.00000675 AC: 1AN: 148256Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 72010
ClinVar
Submissions by phenotype
Intellectual disability, autosomal dominant 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 10, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at