rs4351182

Variant names:

• chr5-88910811-A-C
• rs4351182
• ENST00000514011.6:n.259+5541A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000514011.6(MEF2C-AS1):​n.259+5541A>C variant causes a intron 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 ENST00000514011.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.228
• Publications: 2 publications found

Genes affected

MEF2C-AS1 (HGNC:48908): (MEF2C antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
MEF2C-AS1	NR_104031.1	n.235+5541A>C		intron_variant	Intron 2 of 3
MEF2C-AS1	NR_109940.1	n.307+5038A>C		intron_variant	Intron 3 of 3
MEF2C-AS1	NR_109941.1	n.290+5038A>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MEF2C-AS1	ENST00000514011.6	n.259+5541A>C		intron_variant	Intron 2 of 3	1
MEF2C-AS1	ENST00000506665.1	n.306+5541A>C		intron_variant	Intron 3 of 3	5
MEF2C-AS1	ENST00000508521.2	n.93+5541A>C		intron_variant	Intron 2 of 5	5

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

African (AFR) AF: 0.206 AC: 8523 AN: 41408

American (AMR) AF: 0.254 AC: 3872 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.206 AC: 715 AN: 3470

East Asian (EAS) AF: 0.0815 AC: 422 AN: 5176

South Asian (SAS) AF: 0.202 AC: 969 AN: 4804

European-Finnish (FIN) AF: 0.149 AC: 1574 AN: 10568

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10223 AN: 67972

Other (OTH) AF: 0.197 AC: 417 AN: 2112

Alfa AF: 0.174 Hom.: 1740

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
PhyloP100		-0.23
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs4351182; hg19: chr5-88206628;