15-99664713-C-A

Variant names:

• chr15-99664713-C-A
• rs2033546
• NM_001319206.4:c.259-6610C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001400028.1(MEF2A):​c.259-6610C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.642 in 152,002 control chromosomes in the GnomAD database, including 34,889 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 0.64 (34889 hom., cov: 32)
• Consequence: MEF2A NM_001400028.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.817
• Publications: 7 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.824 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001400028.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MEF2A	NM_001319206.4	MANE Select	c.259-6610C>A		intron	N/A	NP_001306135.1
	MEF2A	NM_001400028.1		c.259-6610C>A		intron	N/A	NP_001386957.1
	MEF2A	NM_001365201.3		c.259-6807C>A		intron	N/A	NP_001352130.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MEF2A	ENST00000557942.6	TSL:5 MANE Select	c.259-6610C>A		intron	N/A	ENSP00000453095.1
	MEF2A	ENST00000354410.9	TSL:1	c.259-6807C>A		intron	N/A	ENSP00000346389.5
	MEF2A	ENST00000947006.1		c.259-6610C>A		intron	N/A	ENSP00000617065.1

Frequencies

GnomAD3 genomes AF: 0.642 AC: 97469 AN: 151884 Hom.: 34865 Cov.: 32

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.919

Gnomad AMR AF: 0.678

Gnomad ASJ AF: 0.846

Gnomad EAS AF: 0.703

Gnomad SAS AF: 0.846

Gnomad FIN AF: 0.799

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.781

Gnomad OTH AF: 0.699

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.642 AC: 97534 AN: 152002 Hom.: 34889 Cov.: 32 AF XY: 0.648 AC XY: 48164 AN XY: 74302

African (AFR) AF: 0.300 AC: 12436 AN: 41402

American (AMR) AF: 0.678 AC: 10359 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.846 AC: 2937 AN: 3470

East Asian (EAS) AF: 0.703 AC: 3638 AN: 5174

South Asian (SAS) AF: 0.846 AC: 4074 AN: 4818

European-Finnish (FIN) AF: 0.799 AC: 8461 AN: 10584

Middle Eastern (MID) AF: 0.857 AC: 252 AN: 294

European-Non Finnish (NFE) AF: 0.781 AC: 53063 AN: 67970

Other (OTH) AF: 0.702 AC: 1478 AN: 2104

Alfa AF: 0.739 Hom.: 147955

Bravo AF: 0.616

Asia WGS AF: 0.750 AC: 2605 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.22
DANN	Benign	0.46
PhyloP100		-0.82
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs2033546; hg19: chr15-100204918;