1-165862412-A-G

Variant names:

• chr1-165862412-A-G
• rs4657482
• NM_012474.5:c.100-27792A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_012474.5(UCK2):​c.100-27792A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.669 in 152,044 control chromosomes in the GnomAD database, including 34,204 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 0.67 (34204 hom., cov: 32)
• Consequence: UCK2 NM_012474.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.05
• Publications: 19 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=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.744 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.100-27792A>G		intron	N/A	NP_036606.2
	UCK2	NM_001363568.2		c.-202-22730A>G		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.100-27792A>G		intron	N/A	ENSP00000356853.4
	UCK2	ENST00000642653.1		c.-202-22730A>G		intron	N/A	ENSP00000494961.1

Frequencies

GnomAD3 genomes AF: 0.669 AC: 101637 AN: 151926 Hom.: 34170 Cov.: 32

Gnomad AFR AF: 0.723

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.640

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.562

Gnomad SAS AF: 0.763

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.661

Gnomad OTH AF: 0.656

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.669 AC: 101721 AN: 152044 Hom.: 34204 Cov.: 32 AF XY: 0.667 AC XY: 49547 AN XY: 74320

African (AFR) AF: 0.723 AC: 29993 AN: 41474

American (AMR) AF: 0.639 AC: 9765 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.553 AC: 1920 AN: 3470

East Asian (EAS) AF: 0.560 AC: 2889 AN: 5158

South Asian (SAS) AF: 0.764 AC: 3680 AN: 4816

European-Finnish (FIN) AF: 0.623 AC: 6579 AN: 10564

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.661 AC: 44896 AN: 67972

Other (OTH) AF: 0.654 AC: 1380 AN: 2110

Alfa AF: 0.660 Hom.: 117864

Bravo AF: 0.668

Asia WGS AF: 0.660 AC: 2299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.22
DANN	Benign	0.40
PhyloP100		-2.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs4657482; hg19: chr1-165831649;