rs3748699

Positions:

• chr1-165908514-G-A
• chr1-165908514-G-C

Variant summary

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

The NM_012474.5(UCK2):​c.*691G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 149,312 control chromosomes in the GnomAD database, including 1,396 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 0.12 (1396 hom., cov: 28)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: UCK2 NM_012474.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.484

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=-0.59).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.156 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UCK2	NM_012474.5	c.*691G>A		3_prime_UTR_variant	7/7	ENST00000367879.9	NP_036606.2
UCK2	NM_001363568.2	c.*691G>A		3_prime_UTR_variant	8/8		NP_001350497.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UCK2	ENST00000367879.9	c.*691G>A		3_prime_UTR_variant	7/7	1	NM_012474.5	ENSP00000356853	P1
UCK2	ENST00000642653.1	c.*691G>A		3_prime_UTR_variant	8/8			ENSP00000494961
UCK2	ENST00000479872.5	n.1565G>A		non_coding_transcript_exon_variant	3/3	2

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18497 AN: 149194 Hom.: 1393 Cov.: 28

Gnomad AFR AF: 0.0412

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.0778

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.132

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.120

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.124 AC: 18507 AN: 149312 Hom.: 1396 Cov.: 28 AF XY: 0.126 AC XY: 9145 AN XY: 72682

Gnomad4 AFR AF: 0.0410

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.144

Gnomad4 EAS AF: 0.0777

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.203

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.121

Alfa AF: 0.149 Hom.: 1978

Bravo AF: 0.115

Asia WGS AF: 0.0900 AC: 311 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	11
DANN	Benign	0.84

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3748699; hg19: chr1-165877751;