1-165904155-T-C

Position:

• chr1-165904155-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_012474.5(UCK2):​c.597+876T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 152,168 control chromosomes in the GnomAD database, including 5,354 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 0.24 (5353 hom., cov: 32)
  • Exomes 𝑓: 0.50 (1 hom.)
• Consequence: UCK2 NM_012474.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.270

Genes affected

UCK2 (HGNC:12562): (uridine-cytidine kinase 2) This gene encodes a pyrimidine ribonucleoside kinase. The encoded protein (EC 2.7.1.48) catalyzes phosphorylation of uridine and cytidine to uridine monophosphate (UMP) and cytidine monophosphate (CMP), respectively.[provided by RefSeq, Oct 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UCK2	NM_012474.5	c.597+876T>C		intron_variant		ENST00000367879.9
UCK2	NM_001363568.2	c.534+876T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UCK2	ENST00000367879.9	c.597+876T>C		intron_variant		1	NM_012474.5	P1

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36811 AN: 152044 Hom.: 5346 Cov.: 32

Gnomad AFR AF: 0.0867

Gnomad AMI AF: 0.375

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.263

GnomAD4 exome AF: 0.500 AC: 3 AN: 6 Hom.: 1 Cov.: 0 AF XY: 0.750 AC XY: 3 AN XY: 4

Gnomad4 FIN exome AF: 0.750

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.242 AC: 36829 AN: 152162 Hom.: 5353 Cov.: 32 AF XY: 0.246 AC XY: 18293 AN XY: 74384

Gnomad4 AFR AF: 0.0866

Gnomad4 AMR AF: 0.294

Gnomad4 ASJ AF: 0.394

Gnomad4 EAS AF: 0.492

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.309

Gnomad4 NFE AF: 0.286

Gnomad4 OTH AF: 0.267

Alfa AF: 0.290 Hom.: 13863

Bravo AF: 0.239

Asia WGS AF: 0.351 AC: 1217 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.3
DANN	Benign	0.58

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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

Other links and lift over

dbSNP: rs3790672; hg19: chr1-165873392;