rs3790665

chr1-165900834-A-C

Variant summary

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

The NM_012474.5(UCK2):c.500-2348A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.24 in 152,234 control chromosomes in the GnomAD database, including 5,260 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 (5260 hom., cov: 33)
• Consequence: UCK2 NM_012474.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.68

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• 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.500-2348A>C		intron_variant		ENST00000367879.9
UCK2	NM_001363568.2	c.437-2348A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UCK2	ENST00000367879.9	c.500-2348A>C		intron_variant		1	NM_012474.5	P1
	ENST00000626270.2	n.162T>G		non_coding_transcript_exon_variant	1/3	5

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36454 AN: 152116 Hom.: 5253 Cov.: 33

Gnomad AFR AF: 0.0859

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.264

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.240 AC: 36472 AN: 152234 Hom.: 5260 Cov.: 33 AF XY: 0.244 AC XY: 18155 AN XY: 74432

Gnomad4 AFR AF: 0.0857

Gnomad4 AMR AF: 0.293

Gnomad4 ASJ AF: 0.393

Gnomad4 EAS AF: 0.492

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.308

Gnomad4 NFE AF: 0.282

Gnomad4 OTH AF: 0.268

Alfa AF: 0.268 Hom.: 2652

Bravo AF: 0.236

Asia WGS AF: 0.350 AC: 1213 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.078
Dann	Benign	0.36
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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

Other links and lift over

dbSNP: rs3790665; hg19: chr1-165870071;