ENST00000531002.3:n.426+6533A>G

Variant names:

• chr11-30603811-A-G
• rs2593549
• ENST00000531002.3:n.426+6533A>G

Variant summary

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

The ENST00000531002.3(MPPED2-AS1):​n.426+6533A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.559 in 150,470 control chromosomes in the GnomAD database, including 24,019 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 0.56 (24019 hom., cov: 26)
• Consequence: MPPED2-AS1 ENST00000531002.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.616
• Publications: 4 publications found

Genes affected

MPPED2-AS1 (HGNC:53909): (MPPED2 antisense RNA 1)

ENSG00000309197 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.647 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000531002.3. 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
	MPPED2-AS1	NR_183760.1		n.277+6533A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MPPED2-AS1	ENST00000531002.3	TSL:4	n.426+6533A>G		intron	N/A
	MPPED2-AS1	ENST00000691848.2		n.446+6533A>G		intron	N/A
	MPPED2-AS1	ENST00000692592.3		n.494+6533A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.558 AC: 83961 AN: 150356 Hom.: 23973 Cov.: 26

Gnomad AFR AF: 0.653

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.645

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.637

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.495

Gnomad OTH AF: 0.533

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

GnomAD4 genome AF: 0.559 AC: 84055 AN: 150470 Hom.: 24019 Cov.: 26 AF XY: 0.562 AC XY: 41234 AN XY: 73432

African (AFR) AF: 0.653 AC: 26683 AN: 40856

American (AMR) AF: 0.645 AC: 9753 AN: 15114

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 1378 AN: 3462

East Asian (EAS) AF: 0.638 AC: 3246 AN: 5090

South Asian (SAS) AF: 0.507 AC: 2412 AN: 4760

European-Finnish (FIN) AF: 0.521 AC: 5364 AN: 10290

Middle Eastern (MID) AF: 0.479 AC: 140 AN: 292

European-Non Finnish (NFE) AF: 0.495 AC: 33441 AN: 67598

Other (OTH) AF: 0.530 AC: 1112 AN: 2098

Alfa AF: 0.517 Hom.: 63380

Bravo AF: 0.575

Asia WGS AF: 0.594 AC: 2062 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.1
DANN	Benign	0.53
PhyloP100		0.62

Splicing

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

Other links and lift over

dbSNP: rs2593549; hg19: chr11-30625358;