chr10-87519366-T-G

Position:

• chr10-87519366-T-G

Variant summary

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

The NM_004897.5(MINPP1):​c.934-1670T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.514 in 152,060 control chromosomes in the GnomAD database, including 21,431 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 0.51 (21431 hom., cov: 32)
• Consequence: MINPP1 NM_004897.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214

Genes affected

MINPP1 (HGNC:7102): (multiple inositol-polyphosphate phosphatase 1) This gene encodes multiple inositol polyphosphate phosphatase; an enzyme that removes 3-phosphate from inositol phosphate substrates. It is the only enzyme known to hydrolzye inositol pentakisphosphate and inositol hexakisphosphate. This enzyme also converts 2,3 bisphosphoglycerate (2,3-BPG) to 2-phosphoglycerate; an activity formerly thought to be exclusive to 2,3-BPG synthase/2-phosphatase (BPGM) in the Rapoport-Luebering shunt of the glycolytic pathway.[provided by RefSeq, Sep 2009]

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 (NFE) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MINPP1	NM_004897.5	c.934-1670T>G		intron_variant		ENST00000371996.9	NP_004888.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MINPP1	ENST00000371996.9	c.934-1670T>G		intron_variant		1	NM_004897.5	ENSP00000361064	P1
MINPP1	ENST00000371994.8	c.835+10833T>G		intron_variant		1		ENSP00000361062
MINPP1	ENST00000536010.1	c.331-1670T>G		intron_variant		1		ENSP00000437823

Frequencies

GnomAD3 genomes AF: 0.514 AC: 78173 AN: 151942 Hom.: 21434 Cov.: 32

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.680

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.611

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.505

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.514 AC: 78204 AN: 152060 Hom.: 21431 Cov.: 32 AF XY: 0.507 AC XY: 37653 AN XY: 74326

Gnomad4 AFR AF: 0.339

Gnomad4 AMR AF: 0.469

Gnomad4 ASJ AF: 0.611

Gnomad4 EAS AF: 0.356

Gnomad4 SAS AF: 0.588

Gnomad4 FIN AF: 0.505

Gnomad4 NFE AF: 0.632

Gnomad4 OTH AF: 0.526

Alfa AF: 0.492 Hom.: 3246

Bravo AF: 0.503

Asia WGS AF: 0.485 AC: 1689 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	2.9
DANN	Benign	0.43

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: rs7896327; hg19: chr10-89279123;