dbSNP rs7905087: PI4K2A:c.923-16A>G (chr10-97662891-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_018425.4(PI4K2A):c.923-16A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.391 in 1,567,704 control chromosomes in the GnomAD database, including 122,466 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 0.41 ( 12941 hom., cov: 32)

Exomes 𝑓: 0.39 ( 109525 hom. )

Consequence

PI4K2A
NM_018425.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.415

Publications

18 publications found

Variant links:

Genes affected

PI4K2A (HGNC:30031): (phosphatidylinositol 4-kinase type 2 alpha) Phosphatidylinositolpolyphosphates (PtdInsPs) are centrally involved in many biologic processes, ranging from cell growth and organization of the actin cytoskeleton to endo- and exocytosis. PI4KII phosphorylates PtdIns at the D-4 position, an essential step in the biosynthesis of PtdInsPs (Barylko et al., 2001 [PubMed 11244087]).[supplied by OMIM, Mar 2008]

PI4K2A links:

ENSG00000249967 (HGNC:):

ENSG00000249967 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.483 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018425.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PI4K2A	NM_018425.4	MANE Select	c.923-16A>G		intron	N/A	NP_060895.1	Q9BTU6

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
PI4K2A	ENST00000370631.4	TSL:1 MANE Select	c.923-16A>G	intron	N/A	ENSP00000359665.3	Q9BTU6
ENSG00000249967	ENST00000370649.3	TSL:2	c.833-16A>G	intron	N/A	ENSP00000359683.3	E9PAM4
PI4K2A	ENST00000880060.1		c.923-16A>G	intron	N/A	ENSP00000550119.1

Frequencies

GnomAD3 genomes

AF:

0.406

AC:

61693

AN:

151986

Hom.:

12915

Cov.:

show subpopulations

Gnomad AFR

AF:

0.488

Gnomad AMI

AF:

0.369

Gnomad AMR

AF:

0.311

Gnomad ASJ

AF:

0.312

Gnomad EAS

AF:

0.345

Gnomad SAS

AF:

0.486

Gnomad FIN

AF:

0.356

Gnomad MID

AF:

0.354

Gnomad NFE

AF:

0.390

Gnomad OTH

AF:

0.384

GnomAD2 exomes

AF:

0.375

AC:

94276

AN:

251258

AF XY:

0.385

show subpopulations

Gnomad AFR exome

AF:

0.482

Gnomad AMR exome

AF:

0.239

Gnomad ASJ exome

AF:

0.317

Gnomad EAS exome

AF:

0.353

Gnomad FIN exome

AF:

0.362

Gnomad NFE exome

AF:

0.380

Gnomad OTH exome

AF:

0.362

GnomAD4 exome

AF:

0.389

AC:

551039

AN:

1415600

Hom.:

109525

Cov.:

AF XY:

0.394

AC XY:

278272

AN XY:

706976

show subpopulations

African (AFR)

AF:

0.489

AC:

15875

AN:

32454

American (AMR)

AF:

0.248

AC:

11065

AN:

44670

Ashkenazi Jewish (ASJ)

AF:

0.311

AC:

8066

AN:

25904

East Asian (EAS)

AF:

0.351

AC:

13870

AN:

39496

South Asian (SAS)

AF:

0.499

AC:

42549

AN:

85218

European-Finnish (FIN)

AF:

0.362

AC:

19298

AN:

53350

Middle Eastern (MID)

AF:

0.360

AC:

2047

AN:

5680

European-Non Finnish (NFE)

AF:

0.388

AC:

415062

AN:

1070018

Other (OTH)

AF:

0.395

AC:

23207

AN:

58810

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.466

Heterozygous variant carriers

14426

28852

43279

57705

72131

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

12802

25604

38406

51208

64010

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.406

AC:

61780

AN:

152104

Hom.:

12941

Cov.:

AF XY:

0.405

AC XY:

30089

AN XY:

74344

show subpopulations

African (AFR)

AF:

0.489

AC:

20281

AN:

41472

American (AMR)

AF:

0.311

AC:

4750

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.312

AC:

1084

AN:

3472

East Asian (EAS)

AF:

0.345

AC:

1790

AN:

5184

South Asian (SAS)

AF:

0.485

AC:

2342

AN:

4824

European-Finnish (FIN)

AF:

0.356

AC:

3763

AN:

10582

Middle Eastern (MID)

AF:

0.367

AC:

108

AN:

294

European-Non Finnish (NFE)

AF:

0.390

AC:

26516

AN:

67982

Other (OTH)

AF:

0.385

AC:

812

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1858

3716

5574

7432

9290

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

598

1196

1794

2392

2990

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.384

Hom.:

17989

Bravo

AF:

0.401

Asia WGS

AF:

0.442

AC:

1536

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.55

(source)

DANN

Benign

0.46

PhyloP100

-0.41

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over