Genetic Variant PI4K2B:c.978+38_978+51delTATATATATATATA (chr4-25260610-TTATATATATATATA-T) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_018323.4(PI4K2B):c.978+38_978+51delTATATATATATATA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00572 in 306,722 control chromosomes in the GnomAD database, including 29 homozygotes. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0050 ( 4 hom., cov: 12)

Exomes 𝑓: 0.0063 ( 25 hom. )

Consequence

PI4K2B
NM_018323.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.68

Publications

0 publications found

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:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BS2

High Homozygotes in GnomAd4 at 4 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018323.4. 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
	PI4K2B	NM_018323.4	MANE Select	c.978+38_978+51delTATATATATATATA		intron	N/A	NP_060793.2	Q8TCG2
	PI4K2B	NR_144633.2		n.1124+38_1124+51delTATATATATATATA		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
PI4K2B	ENST00000264864.8	TSL:1 MANE Select	c.978+20_978+33delTATATATATATATA	intron	N/A	ENSP00000264864.6	Q8TCG2
PI4K2B	ENST00000871538.1		c.978+20_978+33delTATATATATATATA	intron	N/A	ENSP00000541597.1
PI4K2B	ENST00000963199.1		c.963+20_963+33delTATATATATATATA	intron	N/A	ENSP00000633258.1

Frequencies

GnomAD3 genomes

AF:

0.00496

AC:

670

AN:

135092

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00298

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00177

Gnomad ASJ

AF:

0.00814

Gnomad EAS

AF:

0.000219

Gnomad SAS

AF:

0.00453

Gnomad FIN

AF:

0.0103

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00648

Gnomad OTH

AF:

0.00436

GnomAD2 exomes

AF:

0.00723

AC:

267

AN:

36926

AF XY:

0.00769

show subpopulations

Gnomad AFR exome

AF:

0.00443

Gnomad AMR exome

AF:

0.00328

Gnomad ASJ exome

AF:

0.00951

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.0114

Gnomad NFE exome

AF:

0.00663

Gnomad OTH exome

AF:

0.00933

GnomAD4 exome

AF:

0.00630

AC:

1082

AN:

171618

Hom.:

AF XY:

0.00636

AC XY:

607

AN XY:

95428

show subpopulations

African (AFR)

AF:

0.00499

AC:

AN:

4008

American (AMR)

AF:

0.00225

AC:

AN:

7096

Ashkenazi Jewish (ASJ)

AF:

0.00703

AC:

AN:

5402

East Asian (EAS)

AF:

0.000118

AC:

AN:

8494

South Asian (SAS)

AF:

0.00818

AC:

AN:

7584

European-Finnish (FIN)

AF:

0.00818

AC:

201

AN:

24578

Middle Eastern (MID)

AF:

0.0113

AC:

AN:

618

European-Non Finnish (NFE)

AF:

0.00642

AC:

673

AN:

104908

Other (OTH)

AF:

0.00717

AC:

AN:

8930

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.460

Heterozygous variant carriers

125

156

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.00497

AC:

671

AN:

135104

Hom.:

Cov.:

AF XY:

0.00515

AC XY:

333

AN XY:

64608

show subpopulations

African (AFR)

AF:

0.00301

AC:

109

AN:

36254

American (AMR)

AF:

0.00177

AC:

AN:

13008

Ashkenazi Jewish (ASJ)

AF:

0.00814

AC:

AN:

3318

East Asian (EAS)

AF:

0.000220

AC:

AN:

4544

South Asian (SAS)

AF:

0.00455

AC:

AN:

4180

European-Finnish (FIN)

AF:

0.0103

AC:

AN:

6596

Middle Eastern (MID)

AF:

0.00

AC:

AN:

264

European-Non Finnish (NFE)

AF:

0.00648

AC:

416

AN:

64226

Other (OTH)

AF:

0.00432

AC:

AN:

1850

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

116

145

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<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:

0.00195

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

2.7

Mutation Taster

=100/0

polymorphism

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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4-25260610-TTATATATATATATATATATATA-TTATATATA

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