dbSNP rs6834255: PI4K2B:c.*511G>A (chr4-25277698-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_018323.4(PI4K2B):c.*511G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 152,172 control chromosomes in the GnomAD database, including 2,244 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 0.17 ( 2244 hom., cov: 33)

Exomes 𝑓: 0.24 ( 0 hom. )

Consequence

PI4K2B
NM_018323.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.505

Publications

6 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:

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=-0.83).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.298 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
PI4K2B	NM_018323.4 link	c.*511G>A	3_prime_UTR_variant	Exon 10 of 10	ENST00000264864.8	NP_060793.2	Q8TCG2
PI4K2B	NR_144633.2 link	n.2103G>A	non_coding_transcript_exon_variant	Exon 10 of 10
PI4K2B	XM_005248174.3 link	c.*511G>A	3_prime_UTR_variant	Exon 10 of 10		XP_005248231.1
PI4K2B	XM_005248175.5 link	c.*511G>A	3_prime_UTR_variant	Exon 10 of 10		XP_005248232.1	G5E9Z4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PI4K2B	ENST00000264864.8 link	c.*511G>A		3_prime_UTR_variant	Exon 10 of 10	1	NM_018323.4	ENSP00000264864.6		Q8TCG2

Frequencies

GnomAD3 genomes

AF:

0.168

AC:

25547

AN:

151976

Hom.:

2232

Cov.:

show subpopulations

Gnomad AFR

AF:

0.173

Gnomad AMI

AF:

0.0648

Gnomad AMR

AF:

0.185

Gnomad ASJ

AF:

0.156

Gnomad EAS

AF:

0.312

Gnomad SAS

AF:

0.181

Gnomad FIN

AF:

0.134

Gnomad MID

AF:

0.158

Gnomad NFE

AF:

0.157

Gnomad OTH

AF:

0.161

GnomAD4 exome

AF:

0.237

AC:

AN:

Hom.:

Cov.:

AF XY:

0.182

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AF:

0.0833

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.222

AC:

AN:

Other (OTH)

AF:

0.250

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

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:

0.168

AC:

25582

AN:

152092

Hom.:

2244

Cov.:

AF XY:

0.169

AC XY:

12542

AN XY:

74328

show subpopulations

African (AFR)

AF:

0.172

AC:

7155

AN:

41490

American (AMR)

AF:

0.186

AC:

2847

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.156

AC:

540

AN:

3472

East Asian (EAS)

AF:

0.311

AC:

1608

AN:

5178

South Asian (SAS)

AF:

0.181

AC:

874

AN:

4830

European-Finnish (FIN)

AF:

0.134

AC:

1417

AN:

10550

Middle Eastern (MID)

AF:

0.170

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.157

AC:

10688

AN:

67978

Other (OTH)

AF:

0.163

AC:

344

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1088

2176

3264

4352

5440

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

308

616

924

1232

1540

<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:

0.161

Hom.:

7571

Bravo

AF:

0.169

Asia WGS

AF:

0.252

AC:

872

AN:

3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

5.1

(source)

DANN

Benign

0.50

PhyloP100

0.51

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