Variant chr22-20709769-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_058004.4(PI4KA):c.6173+139G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0703 in 417,084 control chromosomes in the GnomAD database, including 7,178 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.033 ( 35 hom., cov: 20)

Exomes 𝑓: 0.080 ( 7143 hom. )

Consequence

PI4KA
NM_058004.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.13

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 -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BP6

Variant 22-20709769-C-T is Benign according to our data. Variant chr22-20709769-C-T is described in ClinVar as [Benign]. Clinvar id is 1266351.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAdExome4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.184 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.6173+139G>A		intron_variant		ENST00000255882.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PI4KA	ENST00000255882.11 linkuse as main transcript	c.6173+139G>A		intron_variant		1	NM_058004.4	P1	P42356-1

Frequencies

GnomAD3 genomes

AF:

0.0331

AC:

2763

AN:

83422

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0364

Gnomad AMI

AF:

0.0423

Gnomad AMR

AF:

0.0316

Gnomad ASJ

AF:

0.0272

Gnomad EAS

AF:

0.0218

Gnomad SAS

AF:

0.0132

Gnomad FIN

AF:

0.0215

Gnomad MID

AF:

0.0313

Gnomad NFE

AF:

0.0362

Gnomad OTH

AF:

0.0475

GnomAD4 exome

AF:

0.0796

AC:

26551

AN:

333624

Hom.:

7143

AF XY:

0.0759

AC XY:

13698

AN XY:

180482

show subpopulations

Gnomad4 AFR exome

AF:

0.159

Gnomad4 AMR exome

AF:

0.190

Gnomad4 ASJ exome

AF:

0.0842

Gnomad4 EAS exome

AF:

0.0823

Gnomad4 SAS exome

AF:

0.0597

Gnomad4 FIN exome

AF:

0.0374

Gnomad4 NFE exome

AF:

0.0777

Gnomad4 OTH exome

AF:

0.0845

GnomAD4 genome

AF:

0.0332

AC:

2769

AN:

83460

Hom.:

Cov.:

AF XY:

0.0342

AC XY:

1399

AN XY:

40954

show subpopulations

Gnomad4 AFR

AF:

0.0365

Gnomad4 AMR

AF:

0.0316

Gnomad4 ASJ

AF:

0.0272

Gnomad4 EAS

AF:

0.0221

Gnomad4 SAS

AF:

0.0135

Gnomad4 FIN

AF:

0.0215

Gnomad4 NFE

AF:

0.0362

Gnomad4 OTH

AF:

0.0470

Alfa

AF:

0.306

Hom.:

760

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Oct 05, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.26

DANN

Benign

0.64

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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