Variant 22-20710913-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_058004.4(PI4KA):c.5924-55T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0717 in 1,599,928 control chromosomes in the GnomAD database, including 3,860 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.068 ( 304 hom., cov: 33)

Exomes 𝑓: 0.072 ( 3556 hom. )

Consequence

PI4KA
NM_058004.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.0110

Variant links:

Genes affected

PI4KA (HGNC:8983): (phosphatidylinositol 4-kinase alpha) This gene encodes a phosphatidylinositol (PI) 4-kinase which catalyzes the first committed step in the biosynthesis of phosphatidylinositol 4,5-bisphosphate. The mammalian PI 4-kinases have been classified into two types, II and III, based on their molecular mass, and modulation by detergent and adenosine. The protein encoded by this gene is a type III enzyme that is not inhibited by adenosine. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Apr 2018]

PI4KA links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP6

Variant 22-20710913-A-G is Benign according to our data. Variant chr22-20710913-A-G is described in ClinVar as [Benign]. Clinvar id is 1293825.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0743 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PI4KA	NM_058004.4 linkuse as main transcript	c.5924-55T>C		intron_variant		ENST00000255882.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PI4KA	ENST00000255882.11 linkuse as main transcript	c.5924-55T>C		intron_variant		1	NM_058004.4	P1	P42356-1

Frequencies

GnomAD3 genomes

AF:

0.0679

AC:

10313

AN:

151986

Hom.:

305

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0634

Gnomad AMI

AF:

0.0659

Gnomad AMR

AF:

0.0610

Gnomad ASJ

AF:

0.0282

Gnomad EAS

AF:

0.0807

Gnomad SAS

AF:

0.0646

Gnomad FIN

AF:

0.0583

Gnomad MID

AF:

0.0443

Gnomad NFE

AF:

0.0751

Gnomad OTH

AF:

0.0651

GnomAD4 exome

AF:

0.0721

AC:

104345

AN:

1447828

Hom.:

3556

Cov.:

AF XY:

0.0715

AC XY:

51579

AN XY:

721064

show subpopulations

Gnomad4 AFR exome

AF:

0.0638

Gnomad4 AMR exome

AF:

0.0730

Gnomad4 ASJ exome

AF:

0.0290

Gnomad4 EAS exome

AF:

0.0661

Gnomad4 SAS exome

AF:

0.0661

Gnomad4 FIN exome

AF:

0.0549

Gnomad4 NFE exome

AF:

0.0751

Gnomad4 OTH exome

AF:

0.0680

GnomAD4 genome

AF:

0.0678

AC:

10317

AN:

152100

Hom.:

304

Cov.:

AF XY:

0.0672

AC XY:

5001

AN XY:

74378

show subpopulations

Gnomad4 AFR

AF:

0.0633

Gnomad4 AMR

AF:

0.0608

Gnomad4 ASJ

AF:

0.0282

Gnomad4 EAS

AF:

0.0807

Gnomad4 SAS

AF:

0.0657

Gnomad4 FIN

AF:

0.0583

Gnomad4 NFE

AF:

0.0751

Gnomad4 OTH

AF:

0.0649

Alfa

AF:

0.0729

Hom.:

Asia WGS

AF:

0.0600

AC:

209

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 09, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

2.4

DANN

Benign

0.31

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over