NM_012474.5:c.*691G>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).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UCK2	NM_012474.5	c.*691G>C		3_prime_UTR_variant	Exon 7 of 7	ENST00000367879.9	NP_036606.2
UCK2	NM_001363568.2	c.*691G>C		3_prime_UTR_variant	Exon 8 of 8		NP_001350497.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UCK2	ENST00000367879.9	c.*691G>C		3_prime_UTR_variant	Exon 7 of 7	1	NM_012474.5	ENSP00000356853.4
UCK2	ENST00000479872.5	n.1565G>C		non_coding_transcript_exon_variant	Exon 3 of 3	2
UCK2	ENST00000642653.1	c.*691G>C		3_prime_UTR_variant	Exon 8 of 8			ENSP00000494961.1

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 v4.3

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;