15-99712504-CCAGCAGCAGCAGCAGCAGCAGCAGCAG-CCAGCAGCAGCAGCAGCAGCAGCAGCAGCAG

Position:

• chr15-99712504-CCAGCAGCAGCAGCAGCAGCAGCAGCAG-CCAGCAGCAGCAGCAGCAGCAGCAGCAGCAG

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_001319206.4(MEF2A):​c.1283_1285dupAGC​(p.Gln428dup) variant causes a disruptive inframe insertion change. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0044 (2 hom., cov: 0)
  • Exomes 𝑓: 0.0029 (3 hom.)
• Consequence: MEF2A NM_001319206.4 disruptive_inframe_insertion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.55

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]

MEF2A (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BS2: High AC in GnomAd4 at 663 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MEF2A	NM_001319206.4	c.1283_1285dupAGC	p.Gln428dup	disruptive_inframe_insertion	12/12	ENST00000557942.6	NP_001306135.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MEF2A	ENST00000557942.6	c.1283_1285dupAGC	p.Gln428dup	disruptive_inframe_insertion	12/12	5	NM_001319206.4	ENSP00000453095.1

Frequencies

GnomAD3 genomes AF: 0.00440 AC: 661 AN: 150280 Hom.: 2 Cov.: 0

Gnomad AFR AF: 0.00887

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00291

Gnomad ASJ AF: 0.00433

Gnomad EAS AF: 0.00236

Gnomad SAS AF: 0.00106

Gnomad FIN AF: 0.000974

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00289

Gnomad OTH AF: 0.00830

GnomAD3 exomes AF: 0.00333 AC: 403 AN: 121148 Hom.: 0 AF XY: 0.00324 AC XY: 208 AN XY: 64250

Gnomad AFR exome AF: 0.0108

Gnomad AMR exome AF: 0.00301

Gnomad ASJ exome AF: 0.00361

Gnomad EAS exome AF: 0.00269

Gnomad SAS exome AF: 0.00282

Gnomad FIN exome AF: 0.00183

Gnomad NFE exome AF: 0.00327

Gnomad OTH exome AF: 0.00265

GnomAD4 exome AF: 0.00285 AC: 3938 AN: 1380958 Hom.: 3 Cov.: 0 AF XY: 0.00278 AC XY: 1896 AN XY: 681030

Gnomad4 AFR exome AF: 0.00919

Gnomad4 AMR exome AF: 0.00294

Gnomad4 ASJ exome AF: 0.00383

Gnomad4 EAS exome AF: 0.00262

Gnomad4 SAS exome AF: 0.00225

Gnomad4 FIN exome AF: 0.00136

Gnomad4 NFE exome AF: 0.00272

Gnomad4 OTH exome AF: 0.00351

GnomAD4 genome AF: 0.00441 AC: 663 AN: 150398 Hom.: 2 Cov.: 0 AF XY: 0.00388 AC XY: 285 AN XY: 73374

Gnomad4 AFR AF: 0.00885

Gnomad4 AMR AF: 0.00290

Gnomad4 ASJ AF: 0.00433

Gnomad4 EAS AF: 0.00237

Gnomad4 SAS AF: 0.00106

Gnomad4 FIN AF: 0.000974

Gnomad4 NFE AF: 0.00289

Gnomad4 OTH AF: 0.00918

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3138597; hg19: chr15-100252709;