rs145475623
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_001378120.1(MBD5):c.3842C>T(p.Thr1281Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000645 in 1,614,206 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001378120.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MBD5 | NM_001378120.1 | c.3842C>T | p.Thr1281Ile | missense_variant | 11/14 | ENST00000642680.2 | NP_001365049.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MBD5 | ENST00000642680.2 | c.3842C>T | p.Thr1281Ile | missense_variant | 11/14 | NM_001378120.1 | ENSP00000493871 |
Frequencies
GnomAD3 genomes AF: 0.000348 AC: 53AN: 152200Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000481 AC: 121AN: 251428Hom.: 0 AF XY: 0.000515 AC XY: 70AN XY: 135884
GnomAD4 exome AF: 0.000676 AC: 988AN: 1461888Hom.: 3 Cov.: 32 AF XY: 0.000701 AC XY: 510AN XY: 727246
GnomAD4 genome AF: 0.000348 AC: 53AN: 152318Hom.: 0 Cov.: 32 AF XY: 0.000295 AC XY: 22AN XY: 74468
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 18, 2020 | This variant is associated with the following publications: (PMID: 17847001, 21981781, 27222293) - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2024 | MBD5: BP4, BS1 - |
Uncertain significance, flagged submission | clinical testing | Eurofins Ntd Llc (ga) | Apr 11, 2017 | - - |
MBD5 associated neurodevelopmental disorder Pathogenic:1
Likely pathogenic, flagged submission | research | Elsea Laboratory, Baylor College of Medicine | Oct 01, 2012 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Feb 25, 2016 | - - |
Intellectual disability, autosomal dominant 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 21, 2024 | - - |
MBD5-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 14, 2020 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 09, 2021 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at