5-89116571-T-C

Variant names:

• chr5-89116571-T-C
• rs10223241
• ENST00000509179.6:n.506+21542T>C

Variant summary

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

The ENST00000509179.6(MEF2C-AS1):​n.506+21542T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 152,172 control chromosomes in the GnomAD database, including 2,197 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 0.15 (2197 hom., cov: 32)
• Consequence: MEF2C-AS1 ENST00000509179.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.635
• Publications: 4 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.212 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MEF2C-AS1	NR_136217.1	n.381+21542T>C		intron_variant	Intron 4 of 6
MEF2C-AS1	NR_136218.1	n.471+21542T>C		intron_variant	Intron 5 of 8
MEF2C-AS1	NR_136219.1	n.364+21542T>C		intron_variant	Intron 4 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MEF2C-AS1	ENST00000509179.6	n.506+21542T>C		intron_variant	Intron 6 of 7	5
MEF2C-AS1	ENST00000512585.5	n.202+21542T>C		intron_variant	Intron 3 of 5	5
MEF2C-AS1	ENST00000514092.5	n.244+21542T>C		intron_variant	Intron 4 of 6	3

Frequencies

GnomAD3 genomes AF: 0.152 AC: 23065 AN: 152054 Hom.: 2197 Cov.: 32

Gnomad AFR AF: 0.0463

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.152 AC: 23056 AN: 152172 Hom.: 2197 Cov.: 32 AF XY: 0.147 AC XY: 10966 AN XY: 74402

African (AFR) AF: 0.0462 AC: 1918 AN: 41556

American (AMR) AF: 0.141 AC: 2160 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.270 AC: 937 AN: 3470

East Asian (EAS) AF: 0.123 AC: 638 AN: 5190

South Asian (SAS) AF: 0.150 AC: 725 AN: 4820

European-Finnish (FIN) AF: 0.138 AC: 1455 AN: 10576

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.215 AC: 14621 AN: 67972

Other (OTH) AF: 0.168 AC: 354 AN: 2110

Alfa AF: 0.203 Hom.: 5496

Bravo AF: 0.149

Asia WGS AF: 0.107 AC: 372 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.40
DANN	Benign	0.52
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs10223241; hg19: chr5-88412388;