rs13103597

chr4-142637428-C-T

Variant summary

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

The NM_001101669.3(INPP4B):c.-191+88411G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 152,018 control chromosomes in the GnomAD database, including 1,381 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 0.13 (1381 hom., cov: 32)
• Consequence: INPP4B NM_001101669.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.99

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.195 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
INPP4B	NM_001101669.3	c.-191+88411G>A		intron_variant		ENST00000262992.9
LOC101927613	XR_007058285.1	n.4456-25037C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
INPP4B	ENST00000262992.9	c.-191+88411G>A		intron_variant		5	NM_001101669.3	P3
	ENST00000509497.1	n.345-23355C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20279 AN: 151896 Hom.: 1374 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.0369

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.185

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.134 AC: 20310 AN: 152018 Hom.: 1381 Cov.: 32 AF XY: 0.134 AC XY: 9952 AN XY: 74294

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.108

Gnomad4 ASJ AF: 0.168

Gnomad4 EAS AF: 0.0370

Gnomad4 SAS AF: 0.206

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.134

Gnomad4 OTH AF: 0.140

Alfa AF: 0.136 Hom.: 178

Bravo AF: 0.132

Asia WGS AF: 0.152 AC: 530 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.13
Dann	Benign	0.46

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: rs13103597; hg19: chr4-143558581;