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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PI4K2A	NM_018425.4 link	c.923-16A>G		intron_variant	Intron 4 of 8	ENST00000370631.4	NP_060895.1	Q9BTU6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PI4K2A	ENST00000370631.4 link	c.923-16A>G		intron_variant	Intron 4 of 8	1	NM_018425.4	ENSP00000359665.3		Q9BTU6
ENSG00000249967	ENST00000370649.3 link	c.833-16A>G		intron_variant	Intron 5 of 9	2		ENSP00000359683.3		E9PAM4

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 v4.3

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over