rs3850653
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001193347.1(MEF2C):c.-239-3539T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 152,174 control chromosomes in the GnomAD database, including 2,778 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.18 ( 2778 hom., cov: 32)
Consequence
MEF2C
NM_001193347.1 intron
NM_001193347.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.486
Genes affected
MEF2C (HGNC:6996): (myocyte enhancer factor 2C) This locus encodes a member of the MADS box transcription enhancer factor 2 (MEF2) family of proteins, which play a role in myogenesis. The encoded protein, MEF2 polypeptide C, has both trans-activating and DNA binding activities. This protein may play a role in maintaining the differentiated state of muscle cells. Mutations and deletions at this locus have been associated with severe cognitive disability, stereotypic movements, epilepsy, and cerebral malformation. Alternatively spliced transcript variants have been described. [provided by RefSeq, Jul 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.63).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.232 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MEF2C | NM_001193347.1 | c.-239-3539T>C | intron_variant | NP_001180276.1 | ||||
MEF2C | NM_001131005.2 | c.-239-3539T>C | intron_variant | NP_001124477.1 | ||||
MEF2C | XM_011543396.4 | c.-239-3539T>C | intron_variant | XP_011541698.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MEF2C | ENST00000340208.9 | c.-239-3539T>C | intron_variant | 1 | ENSP00000340874.5 | |||||
MEF2C | ENST00000424173.6 | c.-239-3539T>C | intron_variant | 1 | ENSP00000389610.2 | |||||
MEF2C-AS1 | ENST00000514011.5 | n.146+1657A>G | intron_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.182 AC: 27657AN: 152056Hom.: 2773 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.182 AC: 27657AN: 152174Hom.: 2778 Cov.: 32 AF XY: 0.179 AC XY: 13348AN XY: 74394
GnomAD4 genome
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638
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at