11-30405528-C-T

Variant names:

• chr11-30405528-C-T
• rs538811
• ENST00000448418.6:c.766+8700G>A

Variant summary

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

The ENST00000448418.6(MPPED2):​c.766+8700G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.913 in 152,208 control chromosomes in the GnomAD database, including 63,514 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 0.91 (63514 hom., cov: 31)
• Consequence: MPPED2 ENST00000448418.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0400
• Publications: 5 publications found

Genes affected

MPPED2 (HGNC:1180): (metallophosphoesterase domain containing 2) Predicted to enable manganese ion binding activity; phosphoric diester hydrolase activity; and purine ribonucleotide binding activity. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MPPED2	NM_001145399.3	c.766+8700G>A		intron_variant	Intron 6 of 6		NP_001138871.1
MPPED2	NM_001377956.1	c.766+8700G>A		intron_variant	Intron 6 of 6		NP_001364885.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MPPED2	ENST00000448418.6	c.766+8700G>A		intron_variant	Intron 6 of 6	1		ENSP00000388258.2

Frequencies

GnomAD3 genomes AF: 0.913 AC: 138917 AN: 152090 Hom.: 63460 Cov.: 31

Gnomad AFR AF: 0.909

Gnomad AMI AF: 0.962

Gnomad AMR AF: 0.941

Gnomad ASJ AF: 0.882

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.846

Gnomad FIN AF: 0.905

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.911

Gnomad OTH AF: 0.909

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

GnomAD4 genome AF: 0.913 AC: 139028 AN: 152208 Hom.: 63514 Cov.: 31 AF XY: 0.913 AC XY: 67909 AN XY: 74400

African (AFR) AF: 0.909 AC: 37744 AN: 41524

American (AMR) AF: 0.941 AC: 14404 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.882 AC: 3060 AN: 3470

East Asian (EAS) AF: 0.997 AC: 5136 AN: 5154

South Asian (SAS) AF: 0.845 AC: 4068 AN: 4812

European-Finnish (FIN) AF: 0.905 AC: 9605 AN: 10610

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.911 AC: 61965 AN: 68018

Other (OTH) AF: 0.910 AC: 1920 AN: 2110

Alfa AF: 0.906 Hom.: 41751

Bravo AF: 0.918

Asia WGS AF: 0.922 AC: 3206 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	11
DANN	Benign	0.58
PhyloP100		0.040
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs538811; hg19: chr11-30427075;