5-89116571-T-C

Position:

• chr5-89116571-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_136218.1(MEF2C-AS1):​n.471+21542T>C variant causes a intron, non coding transcript 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 NR_136218.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.635

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
MEF2C-AS1	NR_136218.1	n.471+21542T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MEF2C-AS1	ENST00000514092.5	n.244+21542T>C		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.0462

Gnomad4 AMR AF: 0.141

Gnomad4 ASJ AF: 0.270

Gnomad4 EAS AF: 0.123

Gnomad4 SAS AF: 0.150

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.215

Gnomad4 OTH AF: 0.168

Alfa AF: 0.209 Hom.: 4619

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10223241; hg19: chr5-88412388;