rs190982

Positions:

• chr5-88927603-G-A
• chr5-88927603-G-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.219-15413G>A 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 0.721 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 NR_136218.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.234

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.891 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MEF2C-AS1	NR_136218.1	n.219-15413G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MEF2C-AS1	ENST00000514092.5	n.98+22333G>A		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.898

Gnomad4 AMR AF: 0.757

Gnomad4 ASJ AF: 0.578

Gnomad4 EAS AF: 0.862

Gnomad4 SAS AF: 0.627

Gnomad4 FIN AF: 0.726

Gnomad4 NFE AF: 0.609

Gnomad4 OTH AF: 0.690

Alfa AF: 0.623 Hom.: 28047

Bravo AF: 0.734

Asia WGS AF: 0.757 AC: 2632 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs190982; hg19: chr5-88223420;