NM_001128928.2:c.-65+2352T>A

Variant names:

• chr2-190351383-T-A
• rs2582753
• NM_001128928.2:c.-65+2352T>A

Variant summary

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

The NM_001128928.2(INPP1):​c.-65+2352T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.752 in 152,140 control chromosomes in the GnomAD database, including 43,442 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 0.75 (43442 hom., cov: 33)
• Consequence: INPP1 NM_001128928.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54
• Publications: 8 publications found

Genes affected

INPP1 (HGNC:6071): (inositol polyphosphate-1-phosphatase) This gene encodes the enzyme inositol polyphosphate-1-phosphatase, one of the enzymes involved in phosphatidylinositol signaling pathways. This enzyme removes the phosphate group at position 1 of the inositol ring from the polyphosphates inositol 1,4-bisphosphate and inositol 1,3,4-trisphophosphate. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.751 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
INPP1	NM_001128928.2	c.-65+2352T>A		intron_variant	Intron 2 of 6	ENST00000392329.7	NP_001122400.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
INPP1	ENST00000392329.7	c.-65+2352T>A		intron_variant	Intron 2 of 6	5	NM_001128928.2	ENSP00000376142.2

Frequencies

GnomAD3 genomes AF: 0.752 AC: 114384 AN: 152022 Hom.: 43418 Cov.: 33

Gnomad AFR AF: 0.750

Gnomad AMI AF: 0.758

Gnomad AMR AF: 0.735

Gnomad ASJ AF: 0.797

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.755

Gnomad FIN AF: 0.872

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.756

Gnomad OTH AF: 0.750

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

GnomAD4 genome AF: 0.752 AC: 114452 AN: 152140 Hom.: 43442 Cov.: 33 AF XY: 0.755 AC XY: 56176 AN XY: 74368

African (AFR) AF: 0.750 AC: 31122 AN: 41504

American (AMR) AF: 0.735 AC: 11225 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.797 AC: 2768 AN: 3472

East Asian (EAS) AF: 0.500 AC: 2587 AN: 5170

South Asian (SAS) AF: 0.754 AC: 3633 AN: 4816

European-Finnish (FIN) AF: 0.872 AC: 9250 AN: 10604

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.756 AC: 51398 AN: 67986

Other (OTH) AF: 0.746 AC: 1574 AN: 2110

Alfa AF: 0.767 Hom.: 5568

Bravo AF: 0.742

Asia WGS AF: 0.664 AC: 2313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.12
DANN	Benign	0.33
PhyloP100		-1.5
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2582753; hg19: chr2-191216109;