rs3790665

Variant names:

• chr1-165900834-A-C
• rs3790665
• NM_012474.5:c.500-2348A>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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]

ENSG00000236364 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
UCK2	NM_012474.5	c.500-2348A>C		intron_variant	Intron 4 of 6	ENST00000367879.9	NP_036606.2
UCK2	NM_001363568.2	c.437-2348A>C		intron_variant	Intron 5 of 7		NP_001350497.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UCK2	ENST00000367879.9	c.500-2348A>C		intron_variant	Intron 4 of 6	1	NM_012474.5	ENSP00000356853.4

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

African (AFR) AF: 0.0857 AC: 3563 AN: 41574

American (AMR) AF: 0.293 AC: 4478 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.393 AC: 1363 AN: 3468

East Asian (EAS) AF: 0.492 AC: 2548 AN: 5180

South Asian (SAS) AF: 0.230 AC: 1112 AN: 4828

European-Finnish (FIN) AF: 0.308 AC: 3256 AN: 10582

Middle Eastern (MID) AF: 0.260 AC: 76 AN: 292

European-Non Finnish (NFE) AF: 0.282 AC: 19169 AN: 67996

Other (OTH) AF: 0.268 AC: 565 AN: 2110

Alfa AF: 0.269 Hom.: 3012

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
PhyloP100		-1.7
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3790665; hg19: chr1-165870071;