rs8032587

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001319206.4(MEF2A):​c.1136+445T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0362 in 152,278 control chromosomes in the GnomAD database, including 332 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 0.036 ( 332 hom., cov: 33)

Consequence

MEF2A
NM_001319206.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0600
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
MEF2ANM_001319206.4 linkuse as main transcriptc.1136+445T>C intron_variant ENST00000557942.6 NP_001306135.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MEF2AENST00000557942.6 linkuse as main transcriptc.1136+445T>C intron_variant 5 NM_001319206.4 ENSP00000453095 Q02078-2

Frequencies

GnomAD3 genomes
AF:
0.0362
AC:
5502
AN:
152160
Hom.:
331
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.125
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0158
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000621
Gnomad FIN
AF:
0.0000941
Gnomad MID
AF:
0.00949
Gnomad NFE
AF:
0.000456
Gnomad OTH
AF:
0.0234
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0362
AC:
5520
AN:
152278
Hom.:
332
Cov.:
33
AF XY:
0.0344
AC XY:
2565
AN XY:
74472
show subpopulations
Gnomad4 AFR
AF:
0.125
Gnomad4 AMR
AF:
0.0158
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000622
Gnomad4 FIN
AF:
0.0000941
Gnomad4 NFE
AF:
0.000456
Gnomad4 OTH
AF:
0.0232
Alfa
AF:
0.0304
Hom.:
39
Bravo
AF:
0.0420
Asia WGS
AF:
0.00895
AC:
31
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
2.9
DANN
Benign
0.74

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.050
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.

Other links and lift over

dbSNP: rs8032587; hg19: chr15-100251410; API