2-98544045-GCACACACA-GCACACA

Variant names:

• chr2-98544045-GCA-G
• rs3217304
• NM_001134225.2:c.949+56_949+57delAC

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001134225.2(INPP4A):​c.949+56_949+57delAC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 1,380,998 control chromosomes in the GnomAD database, including 32,293 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.25 (4730 hom., cov: 24)
  • Exomes 𝑓: 0.25 (27563 hom.)
• Consequence: INPP4A NM_001134225.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48

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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
INPP4A	NM_001134225.2	c.949+56_949+57delAC		intron_variant	Intron 11 of 24	ENST00000409851.8	NP_001127697.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
INPP4A	ENST00000409851.8	c.949+39_949+40delCA		intron_variant	Intron 11 of 24	1	NM_001134225.2	ENSP00000386777.4

Frequencies

GnomAD3 genomes AF: 0.252 AC: 37826 AN: 150268 Hom.: 4727 Cov.: 24

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.293

GnomAD3 exomes AF: 0.320 AC: 34509 AN: 107972 Hom.: 3202 AF XY: 0.323 AC XY: 18360 AN XY: 56910

Gnomad AFR exome AF: 0.282

Gnomad AMR exome AF: 0.335

Gnomad ASJ exome AF: 0.393

Gnomad EAS exome AF: 0.331

Gnomad SAS exome AF: 0.336

Gnomad FIN exome AF: 0.259

Gnomad NFE exome AF: 0.311

Gnomad OTH exome AF: 0.339

GnomAD4 exome AF: 0.254 AC: 312148 AN: 1230620 Hom.: 27563 AF XY: 0.255 AC XY: 154833 AN XY: 606288

Gnomad4 AFR exome AF: 0.238

Gnomad4 AMR exome AF: 0.297

Gnomad4 ASJ exome AF: 0.343

Gnomad4 EAS exome AF: 0.298

Gnomad4 SAS exome AF: 0.274

Gnomad4 FIN exome AF: 0.214

Gnomad4 NFE exome AF: 0.248

Gnomad4 OTH exome AF: 0.272

GnomAD4 genome AF: 0.252 AC: 37860 AN: 150378 Hom.: 4730 Cov.: 24 AF XY: 0.250 AC XY: 18386 AN XY: 73410

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.277

Gnomad4 ASJ AF: 0.338

Gnomad4 EAS AF: 0.295

Gnomad4 SAS AF: 0.294

Gnomad4 FIN AF: 0.200

Gnomad4 NFE AF: 0.253

Gnomad4 OTH AF: 0.291

Bravo AF: 0.256

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: rs3217304; hg19: chr2-99160508;