rs2593549

Positions:

• chr11-30603811-A-G
• chr11-30603811-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_183760.1(MPPED2-AS1):​n.277+6533A>G variant causes a intron, non coding transcript 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 NR_183760.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.616

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MPPED2-AS1	NR_183760.1	n.277+6533A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MPPED2-AS1	ENST00000531002.2	n.297+6533A>G		intron_variant, non_coding_transcript_variant		4
MPPED2-AS1	ENST00000691848.1	n.291+6533A>G		intron_variant, non_coding_transcript_variant
MPPED2-AS1	ENST00000692592.2	n.315+6533A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.653

Gnomad4 AMR AF: 0.645

Gnomad4 ASJ AF: 0.398

Gnomad4 EAS AF: 0.638

Gnomad4 SAS AF: 0.507

Gnomad4 FIN AF: 0.521

Gnomad4 NFE AF: 0.495

Gnomad4 OTH AF: 0.530

Alfa AF: 0.508 Hom.: 41792

Bravo AF: 0.575

Asia WGS AF: 0.594 AC: 2062 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2593549; hg19: chr11-30625358;