rs3217304

chr2-98544045-GCACACA-Gchr2-98544045-GCACACA-GCAchr2-98544045-GCACACA-GCACAchr2-98544045-GCACACA-GCACACACAchr2-98544045-GCACACA-GCACACACACAchr2-98544045-GCACACA-GCACACACACACA

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001134225.2(INPP4A):c.949+52_949+57del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000458 in 1,440,804 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.000020 (0 hom., cov: 24)
  • Exomes 𝑓: 0.000049 (0 hom.)
• Consequence: INPP4A NM_001134225.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.508

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 Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
INPP4A	NM_001134225.2	c.949+52_949+57del		intron_variant		ENST00000409851.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
INPP4A	ENST00000409851.8	c.949+52_949+57del		intron_variant		1	NM_001134225.2

Frequencies

GnomAD3 genomes AF: 0.0000199 AC: 3 AN: 150412 Hom.: 0 Cov.: 24

Gnomad AFR AF: 0.0000246

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000296

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.0000556 AC: 6 AN: 107972 Hom.: 0 AF XY: 0.0000176 AC XY: 1 AN XY: 56910

Gnomad AFR exome AF: 0.000506

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.0000636

Gnomad FIN exome AF: 0.000109

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.000315

GnomAD4 exome AF: 0.0000488 AC: 63 AN: 1290392 Hom.: 0 AF XY: 0.0000519 AC XY: 33 AN XY: 636034

Gnomad4 AFR exome AF: 0.000101

Gnomad4 AMR exome AF: 0.0000298

Gnomad4 ASJ exome AF: 0.0000435

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000411

Gnomad4 FIN exome AF: 0.0000228

Gnomad4 NFE exome AF: 0.0000512

Gnomad4 OTH exome AF: 0.0000373

GnomAD4 genome AF: 0.0000199 AC: 3 AN: 150412 Hom.: 0 Cov.: 24 AF XY: 0.0000136 AC XY: 1 AN XY: 73382

Gnomad4 AFR AF: 0.0000246

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000296

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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;