Variant 4-25260610-TTATATATATA-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2

The NM_018323.4(PI4K2B):c.978+42_978+51del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00836 in 306,464 control chromosomes in the GnomAD database, including 24 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.011 ( 13 hom., cov: 12)

Exomes 𝑓: 0.0059 ( 11 hom. )

Consequence

PI4K2B
NM_018323.4 intron

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.68

Variant links:

Genes affected

PI4K2B (HGNC:18215): (phosphatidylinositol 4-kinase type 2 beta) This gene encodes a member of the type II PI4 kinase protein family. The encoded protein is primarily cytosolic and contributes to overall PI4-kinase activity along with other protein family members. This protein is involved in early T cell activation. [provided by RefSeq, Dec 2016]

PI4K2B links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 4-25260610-TTATATATATA-T is Benign according to our data. Variant chr4-25260610-TTATATATATA-T is described in ClinVar as [Likely_benign]. Clinvar id is 2776149.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0114 (1542/135078) while in subpopulation AFR AF= 0.0161 (585/36248). AF 95% confidence interval is 0.0151. There are 13 homozygotes in gnomad4. There are 750 alleles in male gnomad4 subpopulation. Median coverage is 12. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 13 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
PI4K2B	NM_018323.4 linkuse as main transcript	c.978+42_978+51del	intron_variant	ENST00000264864.8
PI4K2B	XM_005248174.3 linkuse as main transcript	c.963+42_963+51del	intron_variant
PI4K2B	XM_005248175.5 linkuse as main transcript	c.690+42_690+51del	intron_variant
PI4K2B	NR_144633.2 linkuse as main transcript	n.1124+42_1124+51del	intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PI4K2B	ENST00000264864.8 linkuse as main transcript	c.978+42_978+51del		intron_variant		1	NM_018323.4
PI4K2B	ENST00000512921.4 linkuse as main transcript	c.690+42_690+51del		intron_variant		2		P1

Frequencies

GnomAD3 genomes

AF:

0.0114

AC:

1542

AN:

135066

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0162

Gnomad AMI

AF:

0.0278

Gnomad AMR

AF:

0.0112

Gnomad ASJ

AF:

0.0145

Gnomad EAS

AF:

0.00395

Gnomad SAS

AF:

0.0107

Gnomad FIN

AF:

0.00137

Gnomad MID

AF:

0.0175

Gnomad NFE

AF:

0.00982

Gnomad OTH

AF:

0.0169

GnomAD3 exomes

AF:

0.00401

AC:

148

AN:

36926

Hom.:

AF XY:

0.00379

AC XY:

AN XY:

19504

show subpopulations

Gnomad AFR exome

AF:

0.00363

Gnomad AMR exome

AF:

0.00369

Gnomad ASJ exome

AF:

0.0106

Gnomad EAS exome

AF:

0.000996

Gnomad SAS exome

AF:

0.00659

Gnomad FIN exome

AF:

0.000815

Gnomad NFE exome

AF:

0.00553

Gnomad OTH exome

AF:

0.00746

GnomAD4 exome

AF:

0.00595

AC:

1019

AN:

171386

Hom.:

AF XY:

0.00596

AC XY:

568

AN XY:

95292

show subpopulations

Gnomad4 AFR exome

AF:

0.00623

Gnomad4 AMR exome

AF:

0.00452

Gnomad4 ASJ exome

AF:

0.00984

Gnomad4 EAS exome

AF:

0.00200

Gnomad4 SAS exome

AF:

0.00356

Gnomad4 FIN exome

AF:

0.00106

Gnomad4 NFE exome

AF:

0.00719

Gnomad4 OTH exome

AF:

0.00862

GnomAD4 genome

AF:

0.0114

AC:

1542

AN:

135078

Hom.:

Cov.:

AF XY:

0.0116

AC XY:

750

AN XY:

64600

show subpopulations

Gnomad4 AFR

AF:

0.0161

Gnomad4 AMR

AF:

0.0112

Gnomad4 ASJ

AF:

0.0145

Gnomad4 EAS

AF:

0.00396

Gnomad4 SAS

AF:

0.0108

Gnomad4 FIN

AF:

0.00137

Gnomad4 NFE

AF:

0.00983

Gnomad4 OTH

AF:

0.0168

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Dec 28, 2023

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Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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