rs13103597

Variant names:

• chr4-142637428-C-T
• rs13103597
• NM_001101669.3:c.-191+88411G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 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]

ENSG00000249806 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001101669.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	INPP4B	NM_001101669.3	MANE Select	c.-191+88411G>A		intron	N/A	NP_001095139.1
	INPP4B	NM_001331040.1		c.-191+88411G>A		intron	N/A	NP_001317969.1
	INPP4B	NM_001385335.1		c.-190-174702G>A		intron	N/A	NP_001372264.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	INPP4B	ENST00000262992.9	TSL:5 MANE Select	c.-191+88411G>A		intron	N/A	ENSP00000262992.4
	INPP4B	ENST00000513000.5	TSL:1	c.-290+88411G>A		intron	N/A	ENSP00000425487.1
	INPP4B	ENST00000509777.5	TSL:5	c.-191+88411G>A		intron	N/A	ENSP00000422793.1

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

African (AFR) AF: 0.145 AC: 6020 AN: 41474

American (AMR) AF: 0.108 AC: 1647 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.168 AC: 582 AN: 3472

East Asian (EAS) AF: 0.0370 AC: 191 AN: 5166

South Asian (SAS) AF: 0.206 AC: 992 AN: 4814

European-Finnish (FIN) AF: 0.123 AC: 1293 AN: 10536

Middle Eastern (MID) AF: 0.185 AC: 54 AN: 292

European-Non Finnish (NFE) AF: 0.134 AC: 9086 AN: 67996

Other (OTH) AF: 0.140 AC: 295 AN: 2108

Alfa AF: 0.137 Hom.: 189

Bravo AF: 0.132

Asia WGS AF: 0.152 AC: 530 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.13
DANN	Benign	0.46
PhyloP100		-3.0
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: rs13103597; hg19: chr4-143558581;