5-89256597-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.534+106002T>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 0.94 in 152,072 control chromosomes in the GnomAD database, including 67,321 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 0.94 (67321 hom., cov: 32)
• Consequence: MEF2C-AS1 NR_136218.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0560

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MEF2C-AS1	NR_136218.1	n.534+106002T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MEF2C-AS1	ENST00000514092.5	n.245-120686T>C		intron_variant, non_coding_transcript_variant		3
MEF2C-AS1	ENST00000512585.5	n.320-48153T>C		intron_variant, non_coding_transcript_variant		5
MEF2C-AS1	ENST00000684854.1	n.409-21506T>C		intron_variant, non_coding_transcript_variant
MEF2C-AS1	ENST00000685645.1	n.331-21506T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.940 AC: 142857 AN: 151954 Hom.: 67260 Cov.: 32

Gnomad AFR AF: 0.983

Gnomad AMI AF: 0.946

Gnomad AMR AF: 0.965

Gnomad ASJ AF: 0.918

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.967

Gnomad FIN AF: 0.927

Gnomad MID AF: 0.975

Gnomad NFE AF: 0.905

Gnomad OTH AF: 0.950

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

GnomAD4 genome AF: 0.940 AC: 142977 AN: 152072 Hom.: 67321 Cov.: 32 AF XY: 0.943 AC XY: 70074 AN XY: 74322

Gnomad4 AFR AF: 0.983

Gnomad4 AMR AF: 0.964

Gnomad4 ASJ AF: 0.918

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.967

Gnomad4 FIN AF: 0.927

Gnomad4 NFE AF: 0.905

Gnomad4 OTH AF: 0.951

Alfa AF: 0.920 Hom.: 9525

Bravo AF: 0.944

Asia WGS AF: 0.991 AC: 3448 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	3.5
Dann	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6860971; hg19: chr5-88552414;