5-89058858-T-C

Variant names:

• chr5-89058858-T-C
• rs10037512
• ENST00000508521.2:n.356-16238T>C

Variant summary

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

The ENST00000514092.5(MEF2C-AS1):​n.174-36101T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.569 in 151,938 control chromosomes in the GnomAD database, including 26,451 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 0.57 (26451 hom., cov: 31)
• Consequence: MEF2C-AS1 ENST00000514092.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.754
• Publications: 50 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=-0.59).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.798 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000514092.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MEF2C-AS1	NR_136217.1		n.311-36101T>C		intron	N/A
	MEF2C-AS1	NR_136218.1		n.401-36101T>C		intron	N/A
	MEF2C-AS1	NR_136219.1		n.294-36101T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MEF2C-AS1	ENST00000508521.2	TSL:5	n.356-16238T>C		intron	N/A
	MEF2C-AS1	ENST00000509179.6	TSL:5	n.436-36101T>C		intron	N/A
	MEF2C-AS1	ENST00000512585.5	TSL:5	n.132-36101T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86345 AN: 151820 Hom.: 26383 Cov.: 31

Gnomad AFR AF: 0.805

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.579

Gnomad EAS AF: 0.588

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.463

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.569 AC: 86474 AN: 151938 Hom.: 26451 Cov.: 31 AF XY: 0.564 AC XY: 41902 AN XY: 74276

African (AFR) AF: 0.805 AC: 33379 AN: 41452

American (AMR) AF: 0.549 AC: 8371 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.579 AC: 2007 AN: 3468

East Asian (EAS) AF: 0.587 AC: 3026 AN: 5152

South Asian (SAS) AF: 0.425 AC: 2049 AN: 4816

European-Finnish (FIN) AF: 0.415 AC: 4386 AN: 10560

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.463 AC: 31441 AN: 67928

Other (OTH) AF: 0.563 AC: 1190 AN: 2112

Alfa AF: 0.506 Hom.: 82749

Bravo AF: 0.594

Asia WGS AF: 0.528 AC: 1832 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	14
DANN	Benign	0.71
PhyloP100		0.75

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10037512;

hg19: chr5-88354675;