5-88927603-G-A

Variant names:

• chr5-88927603-G-A
• rs190982
• ENST00000514011.6:n.260-15413G>A

Variant summary

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

The ENST00000514011.6(MEF2C-AS1):​n.260-15413G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.721 in 152,114 control chromosomes in the GnomAD database, including 40,820 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 0.72 (40820 hom., cov: 32)
• Consequence: MEF2C-AS1 ENST00000514011.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.234
• Publications: 122 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.891 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000514011.6. 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_104031.1		n.236-15413G>A		intron	N/A
	MEF2C-AS1	NR_109940.1		n.308-13210G>A		intron	N/A
	MEF2C-AS1	NR_109941.1		n.290+21830G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MEF2C-AS1	ENST00000514011.6	TSL:1	n.260-15413G>A		intron	N/A
	MEF2C-AS1	ENST00000506665.1	TSL:5	n.306+22333G>A		intron	N/A
	MEF2C-AS1	ENST00000508521.2	TSL:5	n.94-15413G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.721 AC: 109575 AN: 151996 Hom.: 40761 Cov.: 32

Gnomad AFR AF: 0.898

Gnomad AMI AF: 0.726

Gnomad AMR AF: 0.757

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.862

Gnomad SAS AF: 0.627

Gnomad FIN AF: 0.726

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.609

Gnomad OTH AF: 0.687

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

GnomAD4 genome AF: 0.721 AC: 109694 AN: 152114 Hom.: 40820 Cov.: 32 AF XY: 0.728 AC XY: 54101 AN XY: 74358

African (AFR) AF: 0.898 AC: 37299 AN: 41520

American (AMR) AF: 0.757 AC: 11579 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.578 AC: 2006 AN: 3468

East Asian (EAS) AF: 0.862 AC: 4468 AN: 5186

South Asian (SAS) AF: 0.627 AC: 3023 AN: 4824

European-Finnish (FIN) AF: 0.726 AC: 7666 AN: 10560

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.609 AC: 41355 AN: 67938

Other (OTH) AF: 0.690 AC: 1461 AN: 2116

Alfa AF: 0.647 Hom.: 84532

Bravo AF: 0.734

Asia WGS AF: 0.757 AC: 2632 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.0
DANN	Benign	0.15
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs190982; hg19: chr5-88223420;