Genetic Variant TPRKB:n.439-509_439-508insA (chr2-73729813-C-CT) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The ENST00000463231.5(TPRKB):n.439-509_439-508insA 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 0.013 ( 35 hom., cov: 0)

Exomes 𝑓: 0.017 ( 1 hom. )

Consequence

TPRKB
ENST00000463231.5 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.00700

Variant links:

Genes affected

TPRKB (HGNC:24259): (TP53RK binding protein) Enables protein kinase binding activity. Involved in tRNA threonylcarbamoyladenosine modification. Located in cytosol and nucleus. Part of EKC/KEOPS complex. Implicated in Galloway-Mowat syndrome 5. [provided by Alliance of Genome Resources, Apr 2022]

TPRKB links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0651 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TPRKB	NM_016058.5 link	c.129_130insA		downstream_gene_variant		ENST00000272424.11	NP_057142.1	Q9Y3C4-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TPRKB	ENST00000272424.11 link	c.129_130insA		downstream_gene_variant		1	NM_016058.5	ENSP00000272424.5		Q9Y3C4-1

Frequencies

GnomAD3 genomes

AF:

0.0133

AC:

1874

AN:

140606

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0448

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00621

Gnomad ASJ

AF:

0.000295

Gnomad EAS

AF:

0.000405

Gnomad SAS

AF:

0.000899

Gnomad FIN

AF:

0.000397

Gnomad MID

AF:

0.00336

Gnomad NFE

AF:

0.000982

Gnomad OTH

AF:

0.00876

GnomAD4 exome

AF:

0.0170

AC:

13437

AN:

788412

Hom.:

Cov.:

AF XY:

0.0169

AC XY:

6310

AN XY:

374204

show subpopulations

Gnomad4 AFR exome

AF:

0.0684

Gnomad4 AMR exome

AF:

0.0279

Gnomad4 ASJ exome

AF:

0.0163

Gnomad4 EAS exome

AF:

0.0169

Gnomad4 SAS exome

AF:

0.0189

Gnomad4 FIN exome

AF:

0.0133

Gnomad4 NFE exome

AF:

0.0158

Gnomad4 OTH exome

AF:

0.0172

GnomAD4 genome

AF:

0.0133

AC:

1875

AN:

140600

Hom.:

Cov.:

AF XY:

0.0126

AC XY:

851

AN XY:

67668

show subpopulations

Gnomad4 AFR

AF:

0.0448

Gnomad4 AMR

AF:

0.00620

Gnomad4 ASJ

AF:

0.000295

Gnomad4 EAS

AF:

0.000406

Gnomad4 SAS

AF:

0.000905

Gnomad4 FIN

AF:

0.000397

Gnomad4 NFE

AF:

0.000983

Gnomad4 OTH

AF:

0.00873

ClinVar

Not reported in ClinVar

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.

2-73729813-CTTTTTT-CTTTTTTT

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over