4-25260610-TTATATATATA-T

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+51delTATATATATA 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]

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 HGVSp Effect Exon rank MANE Protein UniProt
PI4K2BNM_018323.4 linkc.978+42_978+51delTATATATATA intron_variant Intron 6 of 9 ENST00000264864.8 NP_060793.2 Q8TCG2
PI4K2BXM_005248174.3 linkc.963+42_963+51delTATATATATA intron_variant Intron 6 of 9 XP_005248231.1
PI4K2BXM_005248175.5 linkc.690+42_690+51delTATATATATA intron_variant Intron 6 of 9 XP_005248232.1 G5E9Z4
PI4K2BNR_144633.2 linkn.1124+42_1124+51delTATATATATA intron_variant Intron 6 of 9

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PI4K2BENST00000264864.8 linkc.978+20_978+29delTATATATATA intron_variant Intron 6 of 9 1 NM_018323.4 ENSP00000264864.6 Q8TCG2
PI4K2BENST00000512921.4 linkc.690+20_690+29delTATATATATA intron_variant Intron 6 of 9 2 ENSP00000423373.1 G5E9Z4

Frequencies

GnomAD3 genomes
AF:
0.0114
AC:
1542
AN:
135066
Hom.:
13
Cov.:
12
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.:
2
AF XY:
0.00379
AC XY:
74
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.:
11
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.:
13
Cov.:
12
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
Mar 07, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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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.

Other links and lift over

dbSNP: rs533544057; hg19: chr4-25262232; API