rs10075941

Variant names:

• chr5-88911072-C-T
• rs10075941
• ENST00000514011.6:n.259+5802C>T

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+5802C>T 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 152,030 control chromosomes in the GnomAD database, including 2,570 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 (2570 hom., cov: 31)
• Consequence: MEF2C-AS1 ENST00000514011.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65
• 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.247 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000514011.6. 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_104031.1		n.235+5802C>T		intron	N/A
	MEF2C-AS1	NR_109940.1		n.307+5299C>T		intron	N/A
	MEF2C-AS1	NR_109941.1		n.290+5299C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MEF2C-AS1	ENST00000514011.6	TSL:1	n.259+5802C>T		intron	N/A
	MEF2C-AS1	ENST00000506665.1	TSL:5	n.306+5802C>T		intron	N/A
	MEF2C-AS1	ENST00000508521.2	TSL:5	n.93+5802C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26930 AN: 151910 Hom.: 2569 Cov.: 31

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.0818

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.148

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: 26961 AN: 152030 Hom.: 2570 Cov.: 31 AF XY: 0.177 AC XY: 13185 AN XY: 74320

African (AFR) AF: 0.206 AC: 8555 AN: 41430

American (AMR) AF: 0.254 AC: 3878 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.206 AC: 715 AN: 3468

East Asian (EAS) AF: 0.0814 AC: 421 AN: 5174

South Asian (SAS) AF: 0.201 AC: 965 AN: 4808

European-Finnish (FIN) AF: 0.148 AC: 1567 AN: 10584

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

European-Non Finnish (NFE) AF: 0.150 AC: 10215 AN: 67990

Other (OTH) AF: 0.198 AC: 417 AN: 2110

Alfa AF: 0.166 Hom.: 311

Bravo AF: 0.190

Asia WGS AF: 0.182 AC: 634 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.33
DANN	Benign	0.50
PhyloP100		-1.7
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: rs10075941; hg19: chr5-88206889;