5-88722571-GAAA-GAAAAAA

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_002397.5(MEF2C):​c.*30_*32dupTTT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000022 in 1,182,710 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 28)
Exomes 𝑓: 0.000022 ( 0 hom. )

Consequence

MEF2C
NM_002397.5 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.815
Variant links:
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]
MEF2C-AS2 (HGNC:53115): (MEF2C antisense RNA 2)

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BS2
High AC in GnomAdExome4 at 26 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MEF2CNM_002397.5 linkc.*30_*32dupTTT 3_prime_UTR_variant Exon 11 of 11 ENST00000504921.7 NP_002388.2 Q06413-1A0A024RAL7

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MEF2CENST00000504921 linkc.*30_*32dupTTT 3_prime_UTR_variant Exon 11 of 11 1 NM_002397.5 ENSP00000421925.5 Q06413-1

Frequencies

GnomAD3 genomes
Cov.:
28
GnomAD4 exome
AF:
0.0000220
AC:
26
AN:
1182710
Hom.:
0
Cov.:
8
AF XY:
0.0000272
AC XY:
16
AN XY:
588916
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.0000576
Gnomad4 ASJ exome
AF:
0.0000474
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000980
Gnomad4 FIN exome
AF:
0.0000458
Gnomad4 NFE exome
AF:
0.0000156
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
28

ClinVar

Not reported in ClinVar

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr5-88018388; API