rs1366594

Variant names:

• chr5-89080244-A-C
• rs1366594
• ENST00000509179.6:n.436-14715A>C

Your query was ambiguous. Multiple possible variants found:

• chr5-89080244-A-C
• chr5-89080244-A-G
• chr5-89080244-A-T

Variant summary

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

The ENST00000514092.5(MEF2C-AS1):​n.174-14715A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.571 in 151,844 control chromosomes in the GnomAD database, including 26,547 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 (26547 hom., cov: 32)
• Consequence: MEF2C-AS1 ENST00000514092.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900
• Publications: 62 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.794 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000514092.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MEF2C-AS1	NR_136217.1		n.311-14715A>C		intron	N/A
	MEF2C-AS1	NR_136218.1		n.401-14715A>C		intron	N/A
	MEF2C-AS1	NR_136219.1		n.294-14715A>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MEF2C-AS1	ENST00000509179.6	TSL:5	n.436-14715A>C		intron	N/A
	MEF2C-AS1	ENST00000512585.5	TSL:5	n.132-14715A>C		intron	N/A
	MEF2C-AS1	ENST00000514092.5	TSL:3	n.174-14715A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.571 AC: 86571 AN: 151728 Hom.: 26478 Cov.: 32

Gnomad AFR AF: 0.801

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.579

Gnomad EAS AF: 0.601

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.571 AC: 86704 AN: 151844 Hom.: 26547 Cov.: 32 AF XY: 0.566 AC XY: 42038 AN XY: 74220

African (AFR) AF: 0.802 AC: 33237 AN: 41458

American (AMR) AF: 0.567 AC: 8624 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.579 AC: 2007 AN: 3466

East Asian (EAS) AF: 0.601 AC: 3104 AN: 5168

South Asian (SAS) AF: 0.425 AC: 2045 AN: 4816

European-Finnish (FIN) AF: 0.416 AC: 4389 AN: 10546

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.464 AC: 31491 AN: 67876

Other (OTH) AF: 0.563 AC: 1183 AN: 2100

Alfa AF: 0.504 Hom.: 66755

Bravo AF: 0.597

Asia WGS AF: 0.529 AC: 1832 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.6
DANN	Benign	0.38
PhyloP100		0.0090

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1366594;

hg19: chr5-88376061;