rs13102150

Variant names:

• chr4-142548980-C-A
• rs13102150
• NM_001101669.3:c.-190-86254G>T

Variant summary

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

The NM_001101669.3(INPP4B):​c.-190-86254G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.355 in 151,820 control chromosomes in the GnomAD database, including 12,048 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 0.35 (12048 hom., cov: 30)
• Consequence: INPP4B NM_001101669.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.127
• Publications: 5 publications found

Genes affected

INPP4B (HGNC:6075): (inositol polyphosphate-4-phosphatase type II B) INPP4B encodes the inositol polyphosphate 4-phosphatase type II, one of the enzymes involved in phosphatidylinositol signaling pathways. This enzyme removes the phosphate group at position 4 of the inositol ring from inositol 3,4-bisphosphate. There is limited data to suggest that the human type II enzyme is subject to alternative splicing, as has been established for the type I enzyme. [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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.509 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
INPP4B	NM_001101669.3	c.-190-86254G>T		intron_variant	Intron 2 of 25	ENST00000262992.9	NP_001095139.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
INPP4B	ENST00000262992.9	c.-190-86254G>T		intron_variant	Intron 2 of 25	5	NM_001101669.3	ENSP00000262992.4

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53852 AN: 151704 Hom.: 12051 Cov.: 30

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.696

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.0324

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.355 AC: 53836 AN: 151820 Hom.: 12048 Cov.: 30 AF XY: 0.346 AC XY: 25655 AN XY: 74196

African (AFR) AF: 0.118 AC: 4877 AN: 41376

American (AMR) AF: 0.299 AC: 4545 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 1662 AN: 3470

East Asian (EAS) AF: 0.0319 AC: 165 AN: 5170

South Asian (SAS) AF: 0.368 AC: 1772 AN: 4812

European-Finnish (FIN) AF: 0.413 AC: 4349 AN: 10534

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.513 AC: 34857 AN: 67924

Other (OTH) AF: 0.401 AC: 845 AN: 2106

Alfa AF: 0.432 Hom.: 3640

Bravo AF: 0.334

Asia WGS AF: 0.204 AC: 713 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.9
DANN	Benign	0.70
PhyloP100		-0.13
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: rs13102150; hg19: chr4-143470133;