rs4351182

Positions:

• chr5-88910811-A-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.218+5541A>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 0.177 in 151,976 control chromosomes in the GnomAD database, including 2,569 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 0.18 (2569 hom., cov: 31)
• Consequence: MEF2C-AS1 NR_136218.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.228

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 (AMR) allele frequency at 95% confidence interval = 0.247 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MEF2C-AS1	NR_136218.1	n.218+5541A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MEF2C-AS1	ENST00000514092.5	n.98+5541A>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26912 AN: 151858 Hom.: 2568 Cov.: 31

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.0819

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.177 AC: 26943 AN: 151976 Hom.: 2569 Cov.: 31 AF XY: 0.177 AC XY: 13181 AN XY: 74288

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.254

Gnomad4 ASJ AF: 0.206

Gnomad4 EAS AF: 0.0815

Gnomad4 SAS AF: 0.202

Gnomad4 FIN AF: 0.149

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.197

Alfa AF: 0.177 Hom.: 822

Bravo AF: 0.190

Asia WGS AF: 0.182 AC: 634 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4351182; hg19: chr5-88206628;