rs244749

chr5-88845145-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002397.5(MEF2C):c.-142-21215A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 152,110 control chromosomes in the GnomAD database, including 10,688 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 0.34 (10688 hom., cov: 32)
• Consequence: MEF2C NM_002397.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.255

Genes affected

MEF2C (HGNC:6996): (myocyte enhancer factor 2C) This locus encodes a member of the MADS box transcription enhancer factor 2 (MEF2) family of proteins, which play a role in myogenesis. The encoded protein, MEF2 polypeptide C, has both trans-activating and DNA binding activities. This protein may play a role in maintaining the differentiated state of muscle cells. Mutations and deletions at this locus have been associated with severe cognitive disability, stereotypic movements, epilepsy, and cerebral malformation. Alternatively spliced transcript variants have been described. [provided by RefSeq, Jul 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.575 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MEF2C	NM_002397.5	c.-142-21215A>G		intron_variant		ENST00000504921.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MEF2C	ENST00000504921.7	c.-142-21215A>G		intron_variant		1	NM_002397.5

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50920 AN: 151992 Hom.: 10669 Cov.: 32

Gnomad AFR AF: 0.582

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.342

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.335 AC: 50988 AN: 152110 Hom.: 10688 Cov.: 32 AF XY: 0.333 AC XY: 24743 AN XY: 74376

Gnomad4 AFR AF: 0.581

Gnomad4 AMR AF: 0.381

Gnomad4 ASJ AF: 0.260

Gnomad4 EAS AF: 0.341

Gnomad4 SAS AF: 0.310

Gnomad4 FIN AF: 0.179

Gnomad4 NFE AF: 0.205

Gnomad4 OTH AF: 0.333

Alfa AF: 0.258 Hom.: 3608

Bravo AF: 0.368

Asia WGS AF: 0.361 AC: 1256 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	2.5
Dann	Benign	0.43

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

Other links and lift over

dbSNP: rs244749; hg19: chr5-88140962;