rs11676357

chr2-98491814-A-G

Variant summary

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

The NM_001134225.2(INPP4A):c.-165-27150A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.481 in 151,980 control chromosomes in the GnomAD database, including 17,929 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 0.48 (17929 hom., cov: 32)
• Consequence: INPP4A NM_001134225.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.346

Genes affected

INPP4A (HGNC:6074): (inositol polyphosphate-4-phosphatase type I A) This gene encodes an Mg++ independent enzyme that hydrolyzes the 4-position phosphate from the inositol ring of phosphatidylinositol 3,4-bisphosphate, inositol 1,3,4-trisphosphate, and inositol 3,4-bisphosphate. Multiple transcript variants encoding distinct isoforms have been described. [provided by RefSeq, Aug 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.521 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
INPP4A	NM_001134225.2	c.-165-27150A>G		intron_variant		ENST00000409851.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
INPP4A	ENST00000409851.8	c.-165-27150A>G		intron_variant		1	NM_001134225.2

Frequencies

GnomAD3 genomes AF: 0.481 AC: 73089 AN: 151862 Hom.: 17927 Cov.: 32

Gnomad AFR AF: 0.527

Gnomad AMI AF: 0.590

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.483

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

GnomAD4 genome AF: 0.481 AC: 73119 AN: 151980 Hom.: 17929 Cov.: 32 AF XY: 0.475 AC XY: 35258 AN XY: 74274

Gnomad4 AFR AF: 0.527

Gnomad4 AMR AF: 0.471

Gnomad4 ASJ AF: 0.462

Gnomad4 EAS AF: 0.269

Gnomad4 SAS AF: 0.480

Gnomad4 FIN AF: 0.372

Gnomad4 NFE AF: 0.488

Gnomad4 OTH AF: 0.481

Alfa AF: 0.486 Hom.: 10016

Bravo AF: 0.488

Asia WGS AF: 0.399 AC: 1388 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	2.0
Dann	Benign	0.52

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: rs11676357; hg19: chr2-99108277;