5-89058858-T-C

Position:

• chr5-89058858-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.401-36101T>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 0.569 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 NR_136218.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.754

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=-0.59).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.798 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MEF2C-AS1	NR_136218.1	n.401-36101T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MEF2C-AS1	ENST00000514092.5	n.174-36101T>C		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.805

Gnomad4 AMR AF: 0.549

Gnomad4 ASJ AF: 0.579

Gnomad4 EAS AF: 0.587

Gnomad4 SAS AF: 0.425

Gnomad4 FIN AF: 0.415

Gnomad4 NFE AF: 0.463

Gnomad4 OTH AF: 0.563

Alfa AF: 0.496 Hom.: 37949

Bravo AF: 0.594

Asia WGS AF: 0.528 AC: 1832 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10037512; hg19: chr5-88354675;