GeneBe

5-88722588-G-T

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_002397.5(MEF2C):​c.*16C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

MEF2C
NM_002397.5 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.177

Publications

2 publications found
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 was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.55).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002397.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
MEF2C
NM_002397.5
MANE Select
c.*16C>A
3_prime_UTR
Exon 11 of 11NP_002388.2
MEF2C
NM_001193347.1
c.*16C>A
3_prime_UTR
Exon 12 of 12NP_001180276.1
MEF2C
NM_001193350.2
c.*16C>A
3_prime_UTR
Exon 11 of 11NP_001180279.1

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
MEF2C
ENST00000504921.7
TSL:1 MANE Select
c.*16C>A
3_prime_UTR
Exon 11 of 11ENSP00000421925.5
MEF2C
ENST00000340208.9
TSL:1
c.*16C>A
3_prime_UTR
Exon 12 of 12ENSP00000340874.5
MEF2C
ENST00000437473.6
TSL:1
c.*16C>A
3_prime_UTR
Exon 11 of 11ENSP00000396219.2

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD2 exomes
AF:
0.00
AC:
0
AN:
230666
AF XY:
0.00
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
0.00
AC:
0
AN:
1425782
Hom.:
0
Cov.:
32
AF XY:
0.00
AC XY:
0
AN XY:
706566
African (AFR)
AF:
0.00
AC:
0
AN:
31368
American (AMR)
AF:
0.00
AC:
0
AN:
38302
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
25016
East Asian (EAS)
AF:
0.00
AC:
0
AN:
39228
South Asian (SAS)
AF:
0.00
AC:
0
AN:
82088
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
52354
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5568
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
1093276
Other (OTH)
AF:
0.00
AC:
0
AN:
58582
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.55
CADD
Benign
11
DANN
Benign
0.82
PhyloP100
-0.18

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

Other links and lift over

dbSNP: rs200087574; hg19: chr5-88018405; API