rs10519659

chr4-142413904-G-C

Variant summary

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

The NM_001101669.3(INPP4B):c.137-8580C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0366 in 152,120 control chromosomes in the GnomAD database, including 140 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 0.037 (140 hom., cov: 32)
• Consequence: INPP4B NM_001101669.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0300

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=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0692 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
INPP4B	NM_001101669.3	c.137-8580C>G		intron_variant		ENST00000262992.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
INPP4B	ENST00000262992.9	c.137-8580C>G		intron_variant		5	NM_001101669.3	P3

Frequencies

GnomAD3 genomes AF: 0.0366 AC: 5565 AN: 152002 Hom.: 139 Cov.: 32

Gnomad AFR AF: 0.00903

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.0728

Gnomad ASJ AF: 0.0329

Gnomad EAS AF: 0.0532

Gnomad SAS AF: 0.0355

Gnomad FIN AF: 0.0308

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0452

Gnomad OTH AF: 0.0456

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

GnomAD4 genome AF: 0.0366 AC: 5571 AN: 152120 Hom.: 140 Cov.: 32 AF XY: 0.0367 AC XY: 2729 AN XY: 74346

Gnomad4 AFR AF: 0.00903

Gnomad4 AMR AF: 0.0728

Gnomad4 ASJ AF: 0.0329

Gnomad4 EAS AF: 0.0531

Gnomad4 SAS AF: 0.0355

Gnomad4 FIN AF: 0.0308

Gnomad4 NFE AF: 0.0452

Gnomad4 OTH AF: 0.0475

Alfa AF: 0.0411 Hom.: 16

Bravo AF: 0.0394

Asia WGS AF: 0.0770 AC: 266 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	6.0
Dann	Benign	0.79

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: rs10519659; hg19: chr4-143335057;