chr1-165904155-T-C

Variant names:

• chr1-165904155-T-C
• rs3790672
• NM_012474.5:c.597+876T>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.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
• Publications: 24 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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_012474.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UCK2	NM_012474.5	MANE Select	c.597+876T>C		intron	N/A	NP_036606.2
	UCK2	NM_001363568.2		c.534+876T>C		intron	N/A	NP_001350497.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UCK2	ENST00000367879.9	TSL:1 MANE Select	c.597+876T>C		intron	N/A	ENSP00000356853.4
	UCK2	ENST00000470820.1	TSL:1	c.147+876T>C		intron	N/A	ENSP00000476327.1
	UCK2	ENST00000462329.5	TSL:1	n.364+876T>C		intron	N/A

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.750 AC: 3 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.0866 AC: 3598 AN: 41552

American (AMR) AF: 0.294 AC: 4491 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.394 AC: 1364 AN: 3466

East Asian (EAS) AF: 0.492 AC: 2542 AN: 5170

South Asian (SAS) AF: 0.230 AC: 1108 AN: 4822

European-Finnish (FIN) AF: 0.309 AC: 3270 AN: 10578

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.286 AC: 19473 AN: 67982

Other (OTH) AF: 0.267 AC: 562 AN: 2106

Alfa AF: 0.280 Hom.: 28017

Bravo AF: 0.239

Asia WGS AF: 0.351 AC: 1217 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.3
DANN	Benign	0.58
PhyloP100		0.27
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3790672; hg19: chr1-165873392;