1-165908514-G-A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• 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: Benign. The variant received -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 rank	MANE	Protein	UniProt
UCK2	NM_012474.5	c.*691G>A		3_prime_UTR_variant	Exon 7 of 7	ENST00000367879.9	NP_036606.2
UCK2	NM_001363568.2	c.*691G>A		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>A		3_prime_UTR_variant	Exon 7 of 7	1	NM_012474.5	ENSP00000356853.4
UCK2	ENST00000479872.5	n.1565G>A		non_coding_transcript_exon_variant	Exon 3 of 3	2
UCK2	ENST00000642653.1	c.*691G>A		3_prime_UTR_variant	Exon 8 of 8			ENSP00000494961.1

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

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) AC: 0 AN: 0

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

African (AFR) AF: 0.0410 AC: 1656 AN: 40360

American (AMR) AF: 0.148 AC: 2207 AN: 14872

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 499 AN: 3454

East Asian (EAS) AF: 0.0777 AC: 394 AN: 5068

South Asian (SAS) AF: 0.117 AC: 552 AN: 4704

European-Finnish (FIN) AF: 0.203 AC: 2013 AN: 9924

Middle Eastern (MID) AF: 0.127 AC: 36 AN: 284

European-Non Finnish (NFE) AF: 0.159 AC: 10761 AN: 67674

Other (OTH) AF: 0.121 AC: 249 AN: 2064

Alfa AF: 0.137 Hom.: 2562

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
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;