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

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_001319206.4(MEF2A):c.1280_1285dupAGCAGC(p.Gln427_Gln428dup) variant causes a disruptive inframe insertion change. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.028 ( 185 hom., cov: 0)

Exomes 𝑓: 0.0031 ( 37 hom. )

Consequence

MEF2A
NM_001319206.4 disruptive_inframe_insertion

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts 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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 15-99712504-C-CCAGCAG is Benign according to our data. Variant chr15-99712504-C-CCAGCAG is described in ClinVar as [Benign]. Clinvar id is 778574.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0908 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_1285dupAGCAGC	p.Gln427_Gln428dup	disruptive_inframe_insertion	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_1285dupAGCAGC	p.Gln427_Gln428dup	disruptive_inframe_insertion	12/12	5	NM_001319206.4	ENSP00000453095.1		Q02078-2

Frequencies

GnomAD3 genomes

AF:

0.0277

AC:

4160

AN:

150260

Hom.:

181

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0931

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0155

Gnomad ASJ

AF:

0.00231

Gnomad EAS

AF:

0.000787

Gnomad SAS

AF:

0.00234

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.000622

Gnomad OTH

AF:

0.0278

GnomAD3 exomes

AF:

0.00711

AC:

861

AN:

121148

Hom.:

AF XY:

0.00565

AC XY:

363

AN XY:

64250

show subpopulations

Gnomad AFR exome

AF:

0.0991

Gnomad AMR exome

AF:

0.00846

Gnomad ASJ exome

AF:

0.00225

Gnomad EAS exome

AF:

0.00110

Gnomad SAS exome

AF:

0.00130

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000968

Gnomad OTH exome

AF:

0.00766

GnomAD4 exome

AF:

0.00311

AC:

4301

AN:

1381108

Hom.:

Cov.:

AF XY:

0.00276

AC XY:

1879

AN XY:

681094

show subpopulations

Gnomad4 AFR exome

AF:

0.0908

Gnomad4 AMR exome

AF:

0.00803

Gnomad4 ASJ exome

AF:

0.00209

Gnomad4 EAS exome

AF:

0.000484

Gnomad4 SAS exome

AF:

0.00114

Gnomad4 FIN exome

AF:

0.0000209

Gnomad4 NFE exome

AF:

0.000445

Gnomad4 OTH exome

AF:

0.00846

GnomAD4 genome

AF:

0.0278

AC:

4178

AN:

150378

Hom.:

185

Cov.:

AF XY:

0.0270

AC XY:

1980

AN XY:

73356

show subpopulations

Gnomad4 AFR

AF:

0.0932

Gnomad4 AMR

AF:

0.0155

Gnomad4 ASJ

AF:

0.00231

Gnomad4 EAS

AF:

0.000789

Gnomad4 SAS

AF:

0.00234

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000622

Gnomad4 OTH

AF:

0.0275

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Dec 31, 2019

- -

Coronary artery disease, autosomal dominant, 1

Benign:1

Benign, criteria provided, single submitter

research

Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center

Dec 12, 2023

- -

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