rs1366594

Positions:

• chr5-89080244-A-C
• chr5-89080244-A-G
• chr5-89080244-A-T

Variant summary

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

The NR_136218.1(MEF2C-AS1):​n.401-14715A>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 0.571 in 151,844 control chromosomes in the GnomAD database, including 26,547 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 (26547 hom., cov: 32)
• Consequence: MEF2C-AS1 NR_136218.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900

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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.794 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MEF2C-AS1	NR_136218.1	n.401-14715A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MEF2C-AS1	ENST00000514092.5	n.174-14715A>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.571 AC: 86571 AN: 151728 Hom.: 26478 Cov.: 32

Gnomad AFR AF: 0.801

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.579

Gnomad EAS AF: 0.601

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.571 AC: 86704 AN: 151844 Hom.: 26547 Cov.: 32 AF XY: 0.566 AC XY: 42038 AN XY: 74220

Gnomad4 AFR AF: 0.802

Gnomad4 AMR AF: 0.567

Gnomad4 ASJ AF: 0.579

Gnomad4 EAS AF: 0.601

Gnomad4 SAS AF: 0.425

Gnomad4 FIN AF: 0.416

Gnomad4 NFE AF: 0.464

Gnomad4 OTH AF: 0.563

Alfa AF: 0.492 Hom.: 29179

Bravo AF: 0.597

Asia WGS AF: 0.529 AC: 1832 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.6
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1366594; hg19: chr5-88376061;