ENST00000511100.5:n.500T>G

Variant names:

• chr5-89031965-T-G
• rs6894139
• ENST00000511100.5:n.500T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000511100.5(MEF2C-AS1):​n.500T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.562 in 152,002 control chromosomes in the GnomAD database, including 25,672 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 0.56 (25672 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: MEF2C-AS1 ENST00000511100.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.290
• Publications: 36 publications found

Genes affected

MEF2C-AS1 (HGNC:48908): (MEF2C antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.779 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000511100.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MEF2C-AS1	NR_109941.1		n.498T>G		non_coding_transcript_exon	Exon 4 of 4
	MEF2C-AS1	NR_136217.1		n.311-62994T>G		intron	N/A
	MEF2C-AS1	NR_136218.1		n.401-62994T>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MEF2C-AS1	ENST00000511100.5	TSL:3	n.500T>G		non_coding_transcript_exon	Exon 4 of 4
	MEF2C-AS1	ENST00000685027.2		n.615T>G		non_coding_transcript_exon	Exon 5 of 5
	MEF2C-AS1	ENST00000691164.1		n.588T>G		non_coding_transcript_exon	Exon 5 of 5

Frequencies

GnomAD3 genomes AF: 0.562 AC: 85285 AN: 151884 Hom.: 25602 Cov.: 32

Gnomad AFR AF: 0.786

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.545

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.463

Gnomad OTH AF: 0.551

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.562 AC: 85416 AN: 152002 Hom.: 25672 Cov.: 32 AF XY: 0.557 AC XY: 41357 AN XY: 74310

African (AFR) AF: 0.786 AC: 32594 AN: 41448

American (AMR) AF: 0.547 AC: 8359 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.576 AC: 1995 AN: 3466

East Asian (EAS) AF: 0.545 AC: 2823 AN: 5180

South Asian (SAS) AF: 0.423 AC: 2034 AN: 4814

European-Finnish (FIN) AF: 0.416 AC: 4389 AN: 10556

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.463 AC: 31427 AN: 67942

Other (OTH) AF: 0.555 AC: 1174 AN: 2114

Alfa AF: 0.505 Hom.: 37224

Bravo AF: 0.586

Asia WGS AF: 0.509 AC: 1763 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.1
DANN	Benign	0.61
PhyloP100		0.29

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6894139; hg19: chr5-88327782;