5-89256597-T-C

Variant names:

• chr5-89256597-T-C
• rs6860971
• ENST00000512585.5:n.320-48153T>C

Variant summary

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

The ENST00000512585.5(MEF2C-AS1):​n.320-48153T>C variant causes a intron 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 ENST00000512585.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0560
• Publications: 1 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000512585.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MEF2C-AS1	NR_136217.1		n.382-120686T>C		intron	N/A
	MEF2C-AS1	NR_136218.1		n.534+106002T>C		intron	N/A
	MEF2C-AS1	NR_136219.1		n.567+52545T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MEF2C-AS1	ENST00000512585.5	TSL:5	n.320-48153T>C		intron	N/A
	MEF2C-AS1	ENST00000514092.5	TSL:3	n.245-120686T>C		intron	N/A
	MEF2C-AS1	ENST00000684854.1		n.409-21506T>C		intron	N/A

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

African (AFR) AF: 0.983 AC: 40810 AN: 41522

American (AMR) AF: 0.964 AC: 14718 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.918 AC: 3185 AN: 3470

East Asian (EAS) AF: 1.00 AC: 5139 AN: 5140

South Asian (SAS) AF: 0.967 AC: 4661 AN: 4820

European-Finnish (FIN) AF: 0.927 AC: 9835 AN: 10606

Middle Eastern (MID) AF: 0.976 AC: 287 AN: 294

European-Non Finnish (NFE) AF: 0.905 AC: 61475 AN: 67940

Other (OTH) AF: 0.951 AC: 2004 AN: 2108

Alfa AF: 0.923 Hom.: 39802

Bravo AF: 0.944

Asia WGS AF: 0.991 AC: 3448 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.5
DANN	Benign	0.26
PhyloP100		0.056

Splicing

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

Other links and lift over

dbSNP: rs6860971; hg19: chr5-88552414;