1-165908514-G-C

Variant names:

• chr1-165908514-G-C
• rs3748699
• NM_012474.5:c.*691G>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_012474.5(UCK2):​c.*691G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 28)
• Consequence: UCK2 NM_012474.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.484
• Publications: 4 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UCK2	NM_012474.5	MANE Select	c.*691G>C		3_prime_UTR	Exon 7 of 7	NP_036606.2
	UCK2	NM_001363568.2		c.*691G>C		3_prime_UTR	Exon 8 of 8	NP_001350497.1	A0A2R8Y653

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UCK2	ENST00000367879.9	TSL:1 MANE Select	c.*691G>C		3_prime_UTR	Exon 7 of 7	ENSP00000356853.4	Q9BZX2-1
	UCK2	ENST00000642653.1		c.*691G>C		3_prime_UTR	Exon 8 of 8	ENSP00000494961.1	A0A2R8Y653
	UCK2	ENST00000940421.1		c.*691G>C		3_prime_UTR	Exon 5 of 5	ENSP00000610480.1

Frequencies

GnomAD3 genomes Cov.: 28

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 28

Alfa AF: 0.00 Hom.: 2562

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	11
DANN	Benign	0.86
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs3748699; hg19: chr1-165877751;