Genetic Variant NM_001134225.2:c.949+56_949+57delAC (chr2-98544045-GCA-G) – ACMG Classification: Benign (-8 pts)

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

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.48

Variant links:

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]

INPP4A links:

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ACMG classification

Classification made for transcript

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 link	c.949+56_949+57delAC		intron_variant	Intron 11 of 24	ENST00000409851.8	NP_001127697.1	Q96PE3-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
INPP4A	ENST00000409851.8 link	c.949+39_949+40delCA		intron_variant	Intron 11 of 24	1	NM_001134225.2	ENSP00000386777.4		Q96PE3-3

Frequencies

GnomAD3 genomes

AF:

0.252

AC:

37826

AN:

150268

Hom.:

4727

Cov.:

show subpopulations

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

show subpopulations

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

show subpopulations

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.:

AF XY:

0.250

AC XY:

18386

AN XY:

73410

show subpopulations

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

Name

Calibrated prediction

Score

Prediction

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over