ENST00000264093:c.-39_-25delCTCTCGGCGGAAGTG

Variant names:

• chr2-73926861-GGGCGGAAGTGCTCTC-G
• rs759288670
• ENST00000264093:c.-39_-25delCTCTCGGCGGAAGTG

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_Moderate BS2

The ENST00000264093(DGUOK):​c.-39_-25delCTCTCGGCGGAAGTG variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00159 in 1,611,394 control chromosomes in the GnomAD database, including 3 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.0012 (1 hom., cov: 33)
  • Exomes 𝑓: 0.0016 (2 hom.)
• Consequence: DGUOK ENST00000264093 5_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 3.58

Genes affected

DGUOK (HGNC:2858): (deoxyguanosine kinase) In mammalian cells, the phosphorylation of purine deoxyribonucleosides is mediated predominantly by two deoxyribonucleoside kinases, cytosolic deoxycytidine kinase and mitochondrial deoxyguanosine kinase. The protein encoded by this gene is responsible for phosphorylation of purine deoxyribonucleosides in the mitochondrial matrix. In addition, this protein phosphorylates several purine deoxyribonucleoside analogs used in the treatment of lymphoproliferative disorders, and this phosphorylation is critical for the effectiveness of the analogs. Alternative splice variants encoding different protein isoforms have been described for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• BP6: Variant 2-73926861-GGGCGGAAGTGCTCTC-G is Benign according to our data. Variant chr2-73926861-GGGCGGAAGTGCTCTC-G is described in ClinVar as [Benign]. Clinvar id is 1234715.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAdExome4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DGUOK	NM_080916.3	c.-49_-35delGGCGGAAGTGCTCTC		upstream_gene_variant		ENST00000264093.9	NP_550438.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DGUOK	ENST00000264093	c.-39_-25delCTCTCGGCGGAAGTG		5_prime_UTR_variant	Exon 1 of 7	1	NM_080916.3	ENSP00000264093.4
DGUOK	ENST00000264093.9	c.-39_-25delCTCTCGGCGGAAGTG		non_coding_transcript_variant		1	NM_080916.3	ENSP00000264093.4
DGUOK	ENST00000264093.9	c.-49_-35delGGCGGAAGTGCTCTC		upstream_gene_variant		1	NM_080916.3	ENSP00000264093.4

Frequencies

GnomAD3 genomes AF: 0.00117 AC: 178 AN: 152238 Hom.: 1 Cov.: 33

Gnomad AFR AF: 0.000289

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00190

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.000471

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00190

Gnomad OTH AF: 0.000478

GnomAD3 exomes AF: 0.000998 AC: 248 AN: 248588 Hom.: 1 AF XY: 0.00105 AC XY: 142 AN XY: 134774

Gnomad AFR exome AF: 0.000186

Gnomad AMR exome AF: 0.00136

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000163

Gnomad FIN exome AF: 0.000305

Gnomad NFE exome AF: 0.00163

Gnomad OTH exome AF: 0.000492

GnomAD4 exome AF: 0.00164 AC: 2387 AN: 1459038 Hom.: 2 AF XY: 0.00163 AC XY: 1181 AN XY: 725944

Gnomad4 AFR exome AF: 0.000299

Gnomad4 AMR exome AF: 0.00125

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000252

Gnomad4 SAS exome AF: 0.000255

Gnomad4 FIN exome AF: 0.000197

Gnomad4 NFE exome AF: 0.00200

Gnomad4 OTH exome AF: 0.00111

GnomAD4 genome AF: 0.00117 AC: 178 AN: 152356 Hom.: 1 Cov.: 33 AF XY: 0.00125 AC XY: 93 AN XY: 74508

Gnomad4 AFR AF: 0.000289

Gnomad4 AMR AF: 0.00189

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000207

Gnomad4 FIN AF: 0.000471

Gnomad4 NFE AF: 0.00190

Gnomad4 OTH AF: 0.000473

Alfa AF: 0.000619 Hom.: 0

Bravo AF: 0.00114

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Mar 03, 2015

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs759288670; hg19: chr2-74153988;