rs2667100

chr4-142054920-A-G

Variant summary

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

The NM_001101669.3(INPP4B):c.2643-26006T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.814 in 151,896 control chromosomes in the GnomAD database, including 52,469 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 0.81 (52469 hom., cov: 31)
• Consequence: INPP4B NM_001101669.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.903

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.916 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
INPP4B	NM_001101669.3	c.2643-26006T>C		intron_variant		ENST00000262992.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
INPP4B	ENST00000262992.9	c.2643-26006T>C		intron_variant		5	NM_001101669.3	P3

Frequencies

GnomAD3 genomes AF: 0.814 AC: 123593 AN: 151776 Hom.: 52457 Cov.: 31

Gnomad AFR AF: 0.548

Gnomad AMI AF: 0.895

Gnomad AMR AF: 0.881

Gnomad ASJ AF: 0.848

Gnomad EAS AF: 0.919

Gnomad SAS AF: 0.897

Gnomad FIN AF: 0.950

Gnomad MID AF: 0.833

Gnomad NFE AF: 0.922

Gnomad OTH AF: 0.829

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

GnomAD4 genome AF: 0.814 AC: 123642 AN: 151896 Hom.: 52469 Cov.: 31 AF XY: 0.818 AC XY: 60757 AN XY: 74266

Gnomad4 AFR AF: 0.548

Gnomad4 AMR AF: 0.882

Gnomad4 ASJ AF: 0.848

Gnomad4 EAS AF: 0.919

Gnomad4 SAS AF: 0.897

Gnomad4 FIN AF: 0.950

Gnomad4 NFE AF: 0.922

Gnomad4 OTH AF: 0.828

Alfa AF: 0.898 Hom.: 82917

Bravo AF: 0.798

Asia WGS AF: 0.871 AC: 3026 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	0.17
Dann	Benign	0.44

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: rs2667100; hg19: chr4-142976073;