2-190354547-A-G

Variant names:

• chr2-190354547-A-G
• rs4853694
• NM_001128928.2:c.-64-5492A>G

Variant summary

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

The NM_001128928.2(INPP1):​c.-64-5492A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.424 in 152,068 control chromosomes in the GnomAD database, including 16,167 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 0.42 (16167 hom., cov: 32)
• Consequence: INPP1 NM_001128928.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0470
• Publications: 5 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.693 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001128928.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	INPP1	NM_001128928.2	MANE Select	c.-64-5492A>G		intron	N/A	NP_001122400.1	Q6IBG4
	INPP1	NM_002194.4		c.-64-5492A>G		intron	N/A	NP_002185.1	Q6IBG4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	INPP1	ENST00000392329.7	TSL:5 MANE Select	c.-64-5492A>G		intron	N/A	ENSP00000376142.2	P49441
	INPP1	ENST00000322522.8	TSL:1	c.-64-5492A>G		intron	N/A	ENSP00000325423.4	P49441
	INPP1	ENST00000889768.1		c.-64-5492A>G		intron	N/A	ENSP00000559827.1

Frequencies

GnomAD3 genomes AF: 0.424 AC: 64365 AN: 151950 Hom.: 16130 Cov.: 32

Gnomad AFR AF: 0.700

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.498

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.424 AC: 64463 AN: 152068 Hom.: 16167 Cov.: 32 AF XY: 0.419 AC XY: 31177 AN XY: 74330

African (AFR) AF: 0.700 AC: 29027 AN: 41462

American (AMR) AF: 0.362 AC: 5539 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 931 AN: 3472

East Asian (EAS) AF: 0.499 AC: 2581 AN: 5170

South Asian (SAS) AF: 0.276 AC: 1331 AN: 4820

European-Finnish (FIN) AF: 0.261 AC: 2756 AN: 10570

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.310 AC: 21045 AN: 67974

Other (OTH) AF: 0.423 AC: 894 AN: 2114

Alfa AF: 0.363 Hom.: 1849

Bravo AF: 0.445

Asia WGS AF: 0.383 AC: 1331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.7
DANN	Benign	0.51
PhyloP100		-0.047
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: rs4853694; hg19: chr2-191219273;