4-25260610-TTATATATATATATATATATATA-TTA

Variant names:

• chr4-25260610-TTATATATATATATATATATA-T
• rs533544057
• NM_018323.4:c.978+32_978+51delTATATATATATATATATATA

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_018323.4(PI4K2B):​c.978+32_978+51delTATATATATATATATATATA variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.000022 (0 hom., cov: 12)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: PI4K2B NM_018323.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.68
• Publications: 0 publications found

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]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

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+32_978+51delTATATATATATATATATATA		intron	N/A	NP_060793.2	Q8TCG2
	PI4K2B	NR_144633.2		n.1124+32_1124+51delTATATATATATATATATATA		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PI4K2B	ENST00000264864.8	TSL:1 MANE Select	c.978+20_978+39delTATATATATATATATATATA		intron	N/A	ENSP00000264864.6	Q8TCG2
	PI4K2B	ENST00000871538.1		c.978+20_978+39delTATATATATATATATATATA		intron	N/A	ENSP00000541597.1
	PI4K2B	ENST00000963199.1		c.963+20_963+39delTATATATATATATATATATA		intron	N/A	ENSP00000633258.1

Frequencies

GnomAD3 genomes AF: 0.0000222 AC: 3 AN: 135096 Hom.: 0 Cov.: 12

Gnomad AFR AF: 0.0000553

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000219

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 171772 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 95528

African (AFR) AF: 0.00 AC: 0 AN: 4018

American (AMR) AF: 0.00 AC: 0 AN: 7098

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 5406

East Asian (EAS) AF: 0.00 AC: 0 AN: 8498

South Asian (SAS) AF: 0.00 AC: 0 AN: 7598

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 24596

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 618

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 105000

Other (OTH) AF: 0.00 AC: 0 AN: 8940

GnomAD4 genome AF: 0.0000222 AC: 3 AN: 135108 Hom.: 0 Cov.: 12 AF XY: 0.00 AC XY: 0 AN XY: 64612

African (AFR) AF: 0.0000552 AC: 2 AN: 36254

American (AMR) AF: 0.00 AC: 0 AN: 13010

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3318

East Asian (EAS) AF: 0.000220 AC: 1 AN: 4544

South Asian (SAS) AF: 0.00 AC: 0 AN: 4180

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6598

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 264

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 64226

Other (OTH) AF: 0.00 AC: 0 AN: 1850

Alfa AF: 0.00 Hom.: 22

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		2.7

Splicing

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

Other links and lift over

dbSNP: rs533544057; hg19: chr4-25262232;