Variant 15-99712504-CCAGCAGCAGCAGCAGCAGCAGCAGCAG-CCAGCAGCAGCAGCAGCAGCAG details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_001319206.4(MEF2A):c.1280_1285delAGCAGC(p.Gln427_Gln428del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.314 in 1,520,352 control chromosomes in the GnomAD database, including 55,836 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.26 ( 6336 hom., cov: 0)

Exomes 𝑓: 0.32 ( 49500 hom. )

Consequence

MEF2A
NM_001319206.4 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:2

Conservation

PhyloP100: 6.55

Variant links:

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 links:

MEF2A (HGNC:):

MEF2A links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 15-99712504-CCAGCAG-C is Benign according to our data. Variant chr15-99712504-CCAGCAG-C is described in ClinVar as [Benign]. Clinvar id is 403080.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MEF2A	NM_001319206.4 linkuse as main transcript	c.1280_1285delAGCAGC	p.Gln427_Gln428del	disruptive_inframe_deletion	12/12	ENST00000557942.6	NP_001306135.1	Q02078-2A0A0S2Z4N0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MEF2A	ENST00000557942.6 linkuse as main transcript	c.1280_1285delAGCAGC	p.Gln427_Gln428del	disruptive_inframe_deletion	12/12	5	NM_001319206.4	ENSP00000453095.1		Q02078-2

Frequencies

GnomAD3 genomes

AF:

0.262

AC:

39321

AN:

150108

Hom.:

6332

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0663

Gnomad AMI

AF:

0.483

Gnomad AMR

AF:

0.224

Gnomad ASJ

AF:

0.371

Gnomad EAS

AF:

0.335

Gnomad SAS

AF:

0.408

Gnomad FIN

AF:

0.390

Gnomad MID

AF:

0.285

Gnomad NFE

AF:

0.345

Gnomad OTH

AF:

0.251

GnomAD3 exomes

AF:

0.324

AC:

39230

AN:

121148

Hom.:

3821

AF XY:

0.334

AC XY:

21443

AN XY:

64250

show subpopulations

Gnomad AFR exome

AF:

0.0634

Gnomad AMR exome

AF:

0.276

Gnomad ASJ exome

AF:

0.362

Gnomad EAS exome

AF:

0.345

Gnomad SAS exome

AF:

0.386

Gnomad FIN exome

AF:

0.382

Gnomad NFE exome

AF:

0.327

Gnomad OTH exome

AF:

0.319

GnomAD4 exome

AF:

0.320

AC:

438038

AN:

1370124

Hom.:

49500

AF XY:

0.322

AC XY:

217168

AN XY:

675480

show subpopulations

Gnomad4 AFR exome

AF:

0.0550

Gnomad4 AMR exome

AF:

0.240

Gnomad4 ASJ exome

AF:

0.340

Gnomad4 EAS exome

AF:

0.314

Gnomad4 SAS exome

AF:

0.366

Gnomad4 FIN exome

AF:

0.353

Gnomad4 NFE exome

AF:

0.326

Gnomad4 OTH exome

AF:

0.300

GnomAD4 genome

AF:

0.262

AC:

39321

AN:

150228

Hom.:

6336

Cov.:

AF XY:

0.264

AC XY:

19376

AN XY:

73292

show subpopulations

Gnomad4 AFR

AF:

0.0662

Gnomad4 AMR

AF:

0.224

Gnomad4 ASJ

AF:

0.371

Gnomad4 EAS

AF:

0.335

Gnomad4 SAS

AF:

0.407

Gnomad4 FIN

AF:

0.390

Gnomad4 NFE

AF:

0.345

Gnomad4 OTH

AF:

0.251

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

MEF2A-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 31, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 28, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over