rs3791809

Variant names:

• chr2-190344992-C-T
• rs3791809
• NM_001128928.2:c.-209+1031C>T

Variant summary

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

The NM_001128928.2(INPP1):​c.-209+1031C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.432 in 152,068 control chromosomes in the GnomAD database, including 17,306 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 0.43 (17306 hom., cov: 33)
• Consequence: INPP1 NM_001128928.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.462
• Publications: 15 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]

LOC124906109 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.589 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
INPP1	NM_001128928.2	c.-209+1031C>T		intron_variant	Intron 1 of 6	ENST00000392329.7	NP_001122400.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
INPP1	ENST00000392329.7	c.-209+1031C>T		intron_variant	Intron 1 of 6	5	NM_001128928.2	ENSP00000376142.2

Frequencies

GnomAD3 genomes AF: 0.433 AC: 65770 AN: 151948 Hom.: 17318 Cov.: 33

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.717

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.570

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.473

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

GnomAD4 genome AF: 0.432 AC: 65745 AN: 152068 Hom.: 17306 Cov.: 33 AF XY: 0.431 AC XY: 32065 AN XY: 74328

African (AFR) AF: 0.148 AC: 6134 AN: 41484

American (AMR) AF: 0.367 AC: 5608 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.717 AC: 2489 AN: 3470

East Asian (EAS) AF: 0.243 AC: 1256 AN: 5178

South Asian (SAS) AF: 0.607 AC: 2924 AN: 4814

European-Finnish (FIN) AF: 0.570 AC: 6015 AN: 10546

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.583 AC: 39632 AN: 67980

Other (OTH) AF: 0.469 AC: 991 AN: 2114

Alfa AF: 0.548 Hom.: 17121

Bravo AF: 0.400

Asia WGS AF: 0.423 AC: 1476 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	8.6
DANN	Benign	0.56
PhyloP100		0.46
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: rs3791809; hg19: chr2-191209718;