4-142217691-C-T

Position:

• chr4-142217691-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.837-8665G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 152,012 control chromosomes in the GnomAD database, including 13,988 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 0.39 (13988 hom., cov: 32)
• Consequence: INPP4B NM_001101669.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.387

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.653 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
INPP4B	NM_001101669.3	c.837-8665G>A		intron_variant		ENST00000262992.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
INPP4B	ENST00000262992.9	c.837-8665G>A		intron_variant		5	NM_001101669.3	P3

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58683 AN: 151894 Hom.: 13981 Cov.: 32

Gnomad AFR AF: 0.0960

Gnomad AMI AF: 0.585

Gnomad AMR AF: 0.510

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.672

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.502

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.386 AC: 58690 AN: 152012 Hom.: 13988 Cov.: 32 AF XY: 0.392 AC XY: 29115 AN XY: 74308

Gnomad4 AFR AF: 0.0957

Gnomad4 AMR AF: 0.509

Gnomad4 ASJ AF: 0.407

Gnomad4 EAS AF: 0.672

Gnomad4 SAS AF: 0.463

Gnomad4 FIN AF: 0.502

Gnomad4 NFE AF: 0.487

Gnomad4 OTH AF: 0.387

Alfa AF: 0.487 Hom.: 26718

Bravo AF: 0.377

Asia WGS AF: 0.538 AC: 1868 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.80

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: rs2627804; hg19: chr4-143138844;