chr9-131530211-T-C

Position:

• chr9-131530211-T-C

Variant summary

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

The NM_031432.5(UCK1):​c.268+275A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0679 in 152,260 control chromosomes in the GnomAD database, including 427 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 0.068 (427 hom., cov: 33)
• Consequence: UCK1 NM_031432.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47

Genes affected

UCK1 (HGNC:14859): (uridine-cytidine kinase 1) This gene encodes a uridine-cytidine kinase that catalyzes the phosphorylation of uridine and cytidine to uridine monophosphate (UMP) and cytidine monophosphate (CMP) but not the phosphorylation of deoxyribonucleosides or purine ribonucleosides. This enzyme can also phosphorylate uridine and cytidine analogs and uses both ATP and GTP as a phosphate donor. Alternative splicing results in multiple splice variants encoding distinct isoforms. [provided by RefSeq, May 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.115 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UCK1	NM_031432.5	c.268+275A>G		intron_variant		ENST00000372215.5	NP_113620.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UCK1	ENST00000372215.5	c.268+275A>G		intron_variant		1	NM_031432.5	ENSP00000361289	P1

Frequencies

GnomAD3 genomes AF: 0.0678 AC: 10321 AN: 152142 Hom.: 425 Cov.: 33

Gnomad AFR AF: 0.0992

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.0571

Gnomad EAS AF: 0.0788

Gnomad SAS AF: 0.0286

Gnomad FIN AF: 0.0224

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0461

Gnomad OTH AF: 0.0759

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

GnomAD4 genome AF: 0.0679 AC: 10339 AN: 152260 Hom.: 427 Cov.: 33 AF XY: 0.0677 AC XY: 5039 AN XY: 74460

Gnomad4 AFR AF: 0.0995

Gnomad4 AMR AF: 0.120

Gnomad4 ASJ AF: 0.0571

Gnomad4 EAS AF: 0.0788

Gnomad4 SAS AF: 0.0284

Gnomad4 FIN AF: 0.0224

Gnomad4 NFE AF: 0.0461

Gnomad4 OTH AF: 0.0747

Alfa AF: 0.0540 Hom.: 313

Bravo AF: 0.0788

Asia WGS AF: 0.0670 AC: 233 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.1
DANN	Benign	0.58

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

Publications

LitVar

Other links and lift over

dbSNP: rs2282010; hg19: chr9-134405598;