rs909270

chr2-190368449-G-Achr2-190368449-G-Cchr2-190368449-G-T

Variant summary

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

The NM_001128928.2(INPP1):c.467-654G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.636 in 151,398 control chromosomes in the GnomAD database, including 31,087 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 0.64 (31087 hom., cov: 32)
• Consequence: INPP1 NM_001128928.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.385

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.74 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
INPP1	NM_001128928.2	c.467-654G>A		intron_variant		ENST00000392329.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
INPP1	ENST00000392329.7	c.467-654G>A		intron_variant		5	NM_001128928.2	P1

Frequencies

GnomAD3 genomes AF: 0.635 AC: 96137 AN: 151278 Hom.: 31042 Cov.: 32

Gnomad AFR AF: 0.724

Gnomad AMI AF: 0.640

Gnomad AMR AF: 0.740

Gnomad ASJ AF: 0.589

Gnomad EAS AF: 0.759

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.548

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.644

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

GnomAD4 genome AF: 0.636 AC: 96237 AN: 151398 Hom.: 31087 Cov.: 32 AF XY: 0.637 AC XY: 47118 AN XY: 74004

Gnomad4 AFR AF: 0.724

Gnomad4 AMR AF: 0.741

Gnomad4 ASJ AF: 0.589

Gnomad4 EAS AF: 0.760

Gnomad4 SAS AF: 0.510

Gnomad4 FIN AF: 0.548

Gnomad4 NFE AF: 0.574

Gnomad4 OTH AF: 0.648

Alfa AF: 0.582 Hom.: 11909

Bravo AF: 0.654

Asia WGS AF: 0.605 AC: 2105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.3
Dann	Benign	0.11

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: rs909270; hg19: chr2-191233175;