rs3824982

Positions:

• chr11-30578198-C-T

Variant summary

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

The NM_001584.3(MPPED2):​c.128+2048G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 152,036 control chromosomes in the GnomAD database, including 2,981 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 (2981 hom., cov: 32)
• Consequence: MPPED2 NM_001584.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.365

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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MPPED2	NM_001584.3	c.128+2048G>A		intron_variant		ENST00000358117.10	NP_001575.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MPPED2	ENST00000358117.10	c.128+2048G>A		intron_variant		1	NM_001584.3	ENSP00000350833.4
MPPED2	ENST00000448418.6	c.128+2048G>A		intron_variant		1		ENSP00000388258.2
MPPED2	ENST00000526437.5	n.128+2048G>A		intron_variant		1		ENSP00000432469.1
MPPED2	ENST00000528686.2	c.128+2048G>A		intron_variant		4		ENSP00000431805.2

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27811 AN: 151918 Hom.: 2974 Cov.: 32

Gnomad AFR AF: 0.0751

Gnomad AMI AF: 0.306

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.201

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.183 AC: 27833 AN: 152036 Hom.: 2981 Cov.: 32 AF XY: 0.182 AC XY: 13552 AN XY: 74310

Gnomad4 AFR AF: 0.0754

Gnomad4 AMR AF: 0.147

Gnomad4 ASJ AF: 0.276

Gnomad4 EAS AF: 0.192

Gnomad4 SAS AF: 0.278

Gnomad4 FIN AF: 0.208

Gnomad4 NFE AF: 0.239

Gnomad4 OTH AF: 0.204

Alfa AF: 0.227 Hom.: 5687

Bravo AF: 0.173

Asia WGS AF: 0.232 AC: 808 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.4
DANN	Benign	0.59

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: rs3824982; hg19: chr11-30599745;