Variant 20-63945638-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_017859.4(UCKL1):c.654+13C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 1,611,604 control chromosomes in the GnomAD database, including 70,416 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.33 ( 9059 hom., cov: 33)

Exomes 𝑓: 0.29 ( 61357 hom. )

Consequence

UCKL1
NM_017859.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.77

Variant links:

Genes affected

UCKL1 (HGNC:15938): (uridine-cytidine kinase 1 like 1) The protein encoded by this gene is a uridine kinase. Uridine kinases catalyze the phosphorylation of uridine to uridine monophosphate. This protein has been shown to bind to Epstein-Barr nuclear antigen 3 as well as natural killer lytic-associated molecule. Ubiquitination of this protein is enhanced by the presence of natural killer lytic-associated molecule. In addition, protein levels decrease in the presence of natural killer lytic-associated molecule, suggesting that association with natural killer lytic-associated molecule results in ubiquitination and subsequent degradation of this protein. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2014]

UCKL1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.487 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UCKL1	NM_017859.4 linkuse as main transcript	c.654+13C>T		intron_variant		ENST00000354216.11

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris	UniProt
UCKL1	ENST00000354216.11 linkuse as main transcript	c.654+13C>T	intron_variant	1	NM_017859.4		Q9NWZ5-1
UCKL1	ENST00000358711.7 linkuse as main transcript	c.654+13C>T	intron_variant	2			Q9NWZ5-2
UCKL1	ENST00000369908.9 linkuse as main transcript	c.609+13C>T	intron_variant	2		P1	Q9NWZ5-4
UCKL1	ENST00000632800.1 linkuse as main transcript	n.541+13C>T	intron_variant, non_coding_transcript_variant	5

Frequencies

GnomAD3 genomes

AF:

0.332

AC:

50406

AN:

151982

Hom.:

9042

Cov.:

show subpopulations

Gnomad AFR

AF:

0.492

Gnomad AMI

AF:

0.218

Gnomad AMR

AF:

0.227

Gnomad ASJ

AF:

0.271

Gnomad EAS

AF:

0.318

Gnomad SAS

AF:

0.278

Gnomad FIN

AF:

0.252

Gnomad MID

AF:

0.272

Gnomad NFE

AF:

0.280

Gnomad OTH

AF:

0.304

GnomAD3 exomes

AF:

0.283

AC:

70678

AN:

249756

Hom.:

10741

AF XY:

0.279

AC XY:

37834

AN XY:

135490

show subpopulations

Gnomad AFR exome

AF:

0.499

Gnomad AMR exome

AF:

0.219

Gnomad ASJ exome

AF:

0.271

Gnomad EAS exome

AF:

0.316

Gnomad SAS exome

AF:

0.282

Gnomad FIN exome

AF:

0.241

Gnomad NFE exome

AF:

0.276

Gnomad OTH exome

AF:

0.275

GnomAD4 exome

AF:

0.286

AC:

417925

AN:

1459504

Hom.:

61357

Cov.:

AF XY:

0.285

AC XY:

206962

AN XY:

725978

show subpopulations

Gnomad4 AFR exome

AF:

0.502

Gnomad4 AMR exome

AF:

0.221

Gnomad4 ASJ exome

AF:

0.269

Gnomad4 EAS exome

AF:

0.325

Gnomad4 SAS exome

AF:

0.278

Gnomad4 FIN exome

AF:

0.238

Gnomad4 NFE exome

AF:

0.284

Gnomad4 OTH exome

AF:

0.291

GnomAD4 genome

AF:

0.332

AC:

50460

AN:

152100

Hom.:

9059

Cov.:

AF XY:

0.328

AC XY:

24354

AN XY:

74342

show subpopulations

Gnomad4 AFR

AF:

0.493

Gnomad4 AMR

AF:

0.227

Gnomad4 ASJ

AF:

0.271

Gnomad4 EAS

AF:

0.317

Gnomad4 SAS

AF:

0.278

Gnomad4 FIN

AF:

0.252

Gnomad4 NFE

AF:

0.280

Gnomad4 OTH

AF:

0.302

Alfa

AF:

0.298

Hom.:

4724

Bravo

AF:

0.336

Asia WGS

AF:

0.316

AC:

1100

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.034

DANN

Benign

0.75

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over