11-30445953-G-A

Position:

• chr11-30445953-G-A

Variant summary

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

The NM_001584.3(MPPED2):​c.537-28320C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 152,126 control chromosomes in the GnomAD database, including 4,128 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 0.21 (4128 hom., cov: 33)
• Consequence: MPPED2 NM_001584.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.363

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MPPED2	NM_001584.3	c.537-28320C>T		intron_variant		ENST00000358117.10	NP_001575.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MPPED2	ENST00000358117.10	c.537-28320C>T		intron_variant		1	NM_001584.3	ENSP00000350833	P1
MPPED2	ENST00000448418.6	c.537-28320C>T		intron_variant		1		ENSP00000388258
MPPED2	ENST00000526437.5	c.*281-28320C>T		intron_variant, NMD_transcript_variant		1		ENSP00000432469
MPPED2	ENST00000524667.5	n.52+22991C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32143 AN: 152008 Hom.: 4125 Cov.: 33

Gnomad AFR AF: 0.0686

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.0680

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.211 AC: 32155 AN: 152126 Hom.: 4128 Cov.: 33 AF XY: 0.209 AC XY: 15566 AN XY: 74352

Gnomad4 AFR AF: 0.0689

Gnomad4 AMR AF: 0.174

Gnomad4 ASJ AF: 0.307

Gnomad4 EAS AF: 0.0681

Gnomad4 SAS AF: 0.226

Gnomad4 FIN AF: 0.297

Gnomad4 NFE AF: 0.296

Gnomad4 OTH AF: 0.219

Alfa AF: 0.268 Hom.: 7568

Bravo AF: 0.195

Asia WGS AF: 0.154 AC: 538 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.4
DANN	Benign	0.74

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs11031093; hg19: chr11-30467500;