4-25260610-TTATATATATATATATATATA-TTATATATATATATATATATATATA

Variant names:

• chr4-25260610-T-TTATA
• rs533544057
• NM_018323.4:c.978+48_978+51dupTATA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

The NM_018323.4(PI4K2B):​c.978+48_978+51dupTATA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.015 (18 hom., cov: 12)
  • Exomes 𝑓: 0.0010 (0 hom.)
• Consequence: PI4K2B NM_018323.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190

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 Benign. Variant got -8 ACMG points.

• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0152 (2048/134850) while in subpopulation SAS AF= 0.0247 (103/4166). AF 95% confidence interval is 0.0209. There are 18 homozygotes in gnomad4. There are 949 alleles in male gnomad4 subpopulation. Median coverage is 12. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 18 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PI4K2B	NM_018323.4	c.978+48_978+51dupTATA		intron_variant	Intron 6 of 9	ENST00000264864.8	NP_060793.2
PI4K2B	XM_005248174.3	c.963+48_963+51dupTATA		intron_variant	Intron 6 of 9		XP_005248231.1
PI4K2B	XM_005248175.5	c.690+48_690+51dupTATA		intron_variant	Intron 6 of 9		XP_005248232.1
PI4K2B	NR_144633.2	n.1124+48_1124+51dupTATA		intron_variant	Intron 6 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PI4K2B	ENST00000264864.8	c.978+19_978+20insTATA		intron_variant	Intron 6 of 9	1	NM_018323.4	ENSP00000264864.6
PI4K2B	ENST00000512921.4	c.690+19_690+20insTATA		intron_variant	Intron 6 of 9	2		ENSP00000423373.1

Frequencies

GnomAD3 genomes AF: 0.0152 AC: 2046 AN: 134838 Hom.: 18 Cov.: 12

Gnomad AFR AF: 0.0139

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.0130

Gnomad ASJ AF: 0.0187

Gnomad EAS AF: 0.0105

Gnomad SAS AF: 0.0241

Gnomad FIN AF: 0.00364

Gnomad MID AF: 0.0246

Gnomad NFE AF: 0.0167

Gnomad OTH AF: 0.0174

GnomAD4 exome AF: 0.00100 AC: 172 AN: 171394 Hom.: 0 Cov.: 0 AF XY: 0.000986 AC XY: 94 AN XY: 95324

Gnomad4 AFR exome AF: 0.00150

Gnomad4 AMR exome AF: 0.000705

Gnomad4 ASJ exome AF: 0.000371

Gnomad4 EAS exome AF: 0.000589

Gnomad4 SAS exome AF: 0.000395

Gnomad4 FIN exome AF: 0.00249

Gnomad4 NFE exome AF: 0.000811

Gnomad4 OTH exome AF: 0.000448

GnomAD4 genome AF: 0.0152 AC: 2048 AN: 134850 Hom.: 18 Cov.: 12 AF XY: 0.0147 AC XY: 949 AN XY: 64486

Gnomad4 AFR AF: 0.0139

Gnomad4 AMR AF: 0.0130

Gnomad4 ASJ AF: 0.0187

Gnomad4 EAS AF: 0.0106

Gnomad4 SAS AF: 0.0247

Gnomad4 FIN AF: 0.00364

Gnomad4 NFE AF: 0.0167

Gnomad4 OTH AF: 0.0173

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;