Genetic Variant NM_001319206.4:c.1434A>G (chr15-99712687-A-G) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_001319206.4(MEF2A):c.1434A>G(p.Pro478Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0842 in 1,561,912 control chromosomes in the GnomAD database, including 6,251 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.063 ( 428 hom., cov: 32)

Exomes 𝑓: 0.087 ( 5823 hom. )

Consequence

MEF2A
NM_001319206.4 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -3.14

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.96).

BP6

Variant 15-99712687-A-G is Benign according to our data. Variant chr15-99712687-A-G is described in ClinVar as [Benign]. Clinvar id is 3056661.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-3.14 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0924 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MEF2A	NM_001319206.4 link	c.1434A>G	p.Pro478Pro	synonymous_variant	Exon 12 of 12	ENST00000557942.6	NP_001306135.1	Q02078-2A0A0S2Z4N0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MEF2A	ENST00000557942.6 link	c.1434A>G	p.Pro478Pro	synonymous_variant	Exon 12 of 12	5	NM_001319206.4	ENSP00000453095.1		Q02078-2

Frequencies

GnomAD3 genomes

AF:

0.0630

AC:

9579

AN:

151940

Hom.:

428

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0245

Gnomad AMI

AF:

0.127

Gnomad AMR

AF:

0.0613

Gnomad ASJ

AF:

0.0888

Gnomad EAS

AF:

0.000577

Gnomad SAS

AF:

0.0268

Gnomad FIN

AF:

0.0464

Gnomad MID

AF:

0.0633

Gnomad NFE

AF:

0.0944

Gnomad OTH

AF:

0.0724

GnomAD3 exomes

AF:

0.0615

AC:

10754

AN:

174956

Hom.:

442

AF XY:

0.0614

AC XY:

5683

AN XY:

92522

show subpopulations

Gnomad AFR exome

AF:

0.0202

Gnomad AMR exome

AF:

0.0451

Gnomad ASJ exome

AF:

0.0896

Gnomad EAS exome

AF:

0.0000816

Gnomad SAS exome

AF:

0.0282

Gnomad FIN exome

AF:

0.0474

Gnomad NFE exome

AF:

0.0931

Gnomad OTH exome

AF:

0.0751

GnomAD4 exome

AF:

0.0865

AC:

121964

AN:

1409854

Hom.:

5823

Cov.:

AF XY:

0.0845

AC XY:

58846

AN XY:

696290

show subpopulations

Gnomad4 AFR exome

AF:

0.0225

Gnomad4 AMR exome

AF:

0.0480

Gnomad4 ASJ exome

AF:

0.0884

Gnomad4 EAS exome

AF:

0.000191

Gnomad4 SAS exome

AF:

0.0298

Gnomad4 FIN exome

AF:

0.0499

Gnomad4 NFE exome

AF:

0.0987

Gnomad4 OTH exome

AF:

0.0812

GnomAD4 genome

AF:

0.0630

AC:

9578

AN:

152058

Hom.:

428

Cov.:

AF XY:

0.0594

AC XY:

4416

AN XY:

74316

show subpopulations

Gnomad4 AFR

AF:

0.0245

Gnomad4 AMR

AF:

0.0612

Gnomad4 ASJ

AF:

0.0888

Gnomad4 EAS

AF:

0.000579

Gnomad4 SAS

AF:

0.0266

Gnomad4 FIN

AF:

0.0464

Gnomad4 NFE

AF:

0.0944

Gnomad4 OTH

AF:

0.0716

Alfa

AF:

0.0820

Hom.:

324

Bravo

AF:

0.0643

Asia WGS

AF:

0.0140

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

MEF2A-related disorder

Benign:1

Nov 12, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

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). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.28

DANN

Benign

0.62

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

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