rs325380
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001319206.4(MEF2A):c.*3642A>C variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.497 in 426,464 control chromosomes in the GnomAD database, including 57,026 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 0.43 ( 16876 hom., cov: 33)
Exomes 𝑓: 0.53 ( 40150 hom. )
Consequence
MEF2A
NM_001319206.4 3_prime_UTR
NM_001319206.4 3_prime_UTR
Scores
1
5
6
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 5.90
Genes affected
MEF2A (HGNC:6993): (myocyte enhancer factor 2A) The protein encoded by this gene is a DNA-binding transcription factor that activates many muscle-specific, growth factor-induced, and stress-induced genes. The encoded protein can act as a homodimer or as a heterodimer and is involved in several cellular processes, including muscle development, neuronal differentiation, cell growth control, and apoptosis. Defects in this gene could be a cause of autosomal dominant coronary artery disease 1 with myocardial infarction (ADCAD1). Several transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Jan 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 (MetaRNN=4.2113662E-4).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.561 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MEF2A | NM_001319206.4 | c.*3642A>C | 3_prime_UTR_variant | 12/12 | ENST00000557942.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MEF2A | ENST00000557942.6 | c.*3642A>C | 3_prime_UTR_variant | 12/12 | 5 | NM_001319206.4 |
Frequencies
GnomAD3 genomes ? AF: 0.434 AC: 65919AN: 151996Hom.: 16873 Cov.: 33
GnomAD3 genomes
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GnomAD3 exomes AF: 0.510 AC: 66764AN: 130936Hom.: 18042 AF XY: 0.518 AC XY: 36923AN XY: 71260
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GnomAD4 exome AF: 0.532 AC: 146070AN: 274350Hom.: 40150 Cov.: 0 AF XY: 0.535 AC XY: 81806AN XY: 152982
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GnomAD4 genome ? AF: 0.433 AC: 65920AN: 152114Hom.: 16876 Cov.: 33 AF XY: 0.433 AC XY: 32164AN XY: 74354
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2066
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ExAC
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8836
Asia WGS
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1394
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationTaster
Benign
P;P;P;P
PROVEAN
Pathogenic
D
REVEL
Uncertain
Vest4
ClinPred
T
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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