4-25260610-TTATATATATATATATATATA-TTATATATATATATA

Variant names:

• chr4-25260610-TTATATA-T
• rs533544057
• NM_018323.4:c.978+46_978+51delTATATA

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_018323.4(PI4K2B):​c.978+46_978+51delTATATA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00513 in 306,114 control chromosomes in the GnomAD database, including 2 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0058 (1 hom., cov: 12)
  • Exomes 𝑓: 0.0046 (1 hom.)
• Consequence: PI4K2B NM_018323.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0360

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

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PI4K2B	NM_018323.4	c.978+46_978+51delTATATA		intron_variant	Intron 6 of 9	ENST00000264864.8	NP_060793.2
PI4K2B	XM_005248174.3	c.963+46_963+51delTATATA		intron_variant	Intron 6 of 9		XP_005248231.1
PI4K2B	XM_005248175.5	c.690+46_690+51delTATATA		intron_variant	Intron 6 of 9		XP_005248232.1
PI4K2B	NR_144633.2	n.1124+46_1124+51delTATATA		intron_variant	Intron 6 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PI4K2B	ENST00000264864.8	c.978+20_978+25delTATATA		intron_variant	Intron 6 of 9	1	NM_018323.4	ENSP00000264864.6
PI4K2B	ENST00000512921.4	c.690+20_690+25delTATATA		intron_variant	Intron 6 of 9	2		ENSP00000423373.1

Frequencies

GnomAD3 genomes AF: 0.00576 AC: 778 AN: 135048 Hom.: 1 Cov.: 12

Gnomad AFR AF: 0.00694

Gnomad AMI AF: 0.0405

Gnomad AMR AF: 0.00492

Gnomad ASJ AF: 0.00814

Gnomad EAS AF: 0.00526

Gnomad SAS AF: 0.00548

Gnomad FIN AF: 0.00152

Gnomad MID AF: 0.00350

Gnomad NFE AF: 0.00509

Gnomad OTH AF: 0.00872

GnomAD3 exomes AF: 0.00260 AC: 96 AN: 36926 Hom.: 1 AF XY: 0.00272 AC XY: 53 AN XY: 19504

Gnomad AFR exome AF: 0.000403

Gnomad AMR exome AF: 0.000820

Gnomad ASJ exome AF: 0.00529

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00412

Gnomad FIN exome AF: 0.00418

Gnomad NFE exome AF: 0.00227

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00462 AC: 791 AN: 171054 Hom.: 1 AF XY: 0.00487 AC XY: 463 AN XY: 95094

Gnomad4 AFR exome AF: 0.00325

Gnomad4 AMR exome AF: 0.00438

Gnomad4 ASJ exome AF: 0.00353

Gnomad4 EAS exome AF: 0.00496

Gnomad4 SAS exome AF: 0.00237

Gnomad4 FIN exome AF: 0.00270

Gnomad4 NFE exome AF: 0.00533

Gnomad4 OTH exome AF: 0.00494

GnomAD4 genome AF: 0.00577 AC: 779 AN: 135060 Hom.: 1 Cov.: 12 AF XY: 0.00565 AC XY: 365 AN XY: 64590

Gnomad4 AFR AF: 0.00696

Gnomad4 AMR AF: 0.00492

Gnomad4 ASJ AF: 0.00814

Gnomad4 EAS AF: 0.00528

Gnomad4 SAS AF: 0.00550

Gnomad4 FIN AF: 0.00152

Gnomad4 NFE AF: 0.00509

Gnomad4 OTH AF: 0.00866

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs533544057; hg19: chr4-25262232;