Genetic Variant TPRKB:n.439-509delA (chr2-73729813-CT-C) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The ENST00000463231.5(TPRKB):n.439-509delA variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.59 ( 24726 hom., cov: 0)

Exomes 𝑓: 0.46 ( 7531 hom. )

Failed GnomAD Quality Control

Consequence

TPRKB
ENST00000463231.5 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

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 -10 ACMG points.

BP6

Variant 2-73729813-CT-C is Benign according to our data. Variant chr2-73729813-CT-C is described in ClinVar as [Benign]. Clinvar id is 1242937.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.676 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TPRKB	NM_016058.5 link	c.*129delA		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.*129delA		downstream_gene_variant		1	NM_016058.5	ENSP00000272424.5		Q9Y3C4-1

Frequencies

GnomAD3 genomes

AF:

0.592

AC:

83157

AN:

140508

Hom.:

24742

Cov.:

show subpopulations

Gnomad AFR

AF:

0.432

Gnomad AMI

AF:

0.758

Gnomad AMR

AF:

0.592

Gnomad ASJ

AF:

0.649

Gnomad EAS

AF:

0.696

Gnomad SAS

AF:

0.674

Gnomad FIN

AF:

0.683

Gnomad MID

AF:

0.664

Gnomad NFE

AF:

0.654

Gnomad OTH

AF:

0.610

GnomAD4 exome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.463

AC:

362461

AN:

782184

Hom.:

7531

Cov.:

AF XY:

0.462

AC XY:

171534

AN XY:

371162

show subpopulations

Gnomad4 AFR exome

AF:

0.393

Gnomad4 AMR exome

AF:

0.397

Gnomad4 ASJ exome

AF:

0.449

Gnomad4 EAS exome

AF:

0.445

Gnomad4 SAS exome

AF:

0.447

Gnomad4 FIN exome

AF:

0.406

Gnomad4 NFE exome

AF:

0.468

Gnomad4 OTH exome

AF:

0.459

GnomAD4 genome

AF:

0.592

AC:

83139

AN:

140502

Hom.:

24726

Cov.:

AF XY:

0.596

AC XY:

40267

AN XY:

67618

show subpopulations

Gnomad4 AFR

AF:

0.432

Gnomad4 AMR

AF:

0.592

Gnomad4 ASJ

AF:

0.649

Gnomad4 EAS

AF:

0.696

Gnomad4 SAS

AF:

0.674

Gnomad4 FIN

AF:

0.683

Gnomad4 NFE

AF:

0.654

Gnomad4 OTH

AF:

0.609

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

May 15, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over