rs116413446
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001378120.1(MBD5):c.1638C>T(p.Ala546Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00382 in 1,613,786 control chromosomes in the GnomAD database, including 24 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001378120.1 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MBD5 | NM_001378120.1 | c.1638C>T | p.Ala546Ala | synonymous_variant | Exon 8 of 14 | ENST00000642680.2 | NP_001365049.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MBD5 | ENST00000642680.2 | c.1638C>T | p.Ala546Ala | synonymous_variant | Exon 8 of 14 | NM_001378120.1 | ENSP00000493871.2 |
Frequencies
GnomAD3 genomes AF: 0.00316 AC: 481AN: 152122Hom.: 4 Cov.: 32
GnomAD3 exomes AF: 0.00403 AC: 1005AN: 249466Hom.: 7 AF XY: 0.00411 AC XY: 555AN XY: 134936
GnomAD4 exome AF: 0.00389 AC: 5679AN: 1461546Hom.: 20 Cov.: 33 AF XY: 0.00373 AC XY: 2715AN XY: 727066
GnomAD4 genome AF: 0.00316 AC: 481AN: 152240Hom.: 4 Cov.: 32 AF XY: 0.00341 AC XY: 254AN XY: 74418
ClinVar
Submissions by phenotype
not provided Benign:4
MBD5: BP4, BP7, BS2 -
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not specified Benign:3
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This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Intellectual disability, autosomal dominant 1 Benign:2
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Inborn genetic diseases Benign:1
This alteration is classified as 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