rs1803484
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_000788.3(DCK):c.*1248A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0214 in 152,224 control chromosomes in the GnomAD database, including 55 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 0.021 ( 55 hom., cov: 33)
Failed GnomAD Quality Control
Consequence
DCK
NM_000788.3 3_prime_UTR
NM_000788.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.00
Genes affected
DCK (HGNC:2704): (deoxycytidine kinase) Deoxycytidine kinase (DCK) is required for the phosphorylation of several deoxyribonucleosides and their nucleoside analogs. Deficiency of DCK is associated with resistance to antiviral and anticancer chemotherapeutic agents. Conversely, increased deoxycytidine kinase activity is associated with increased activation of these compounds to cytotoxic nucleoside triphosphate derivatives. DCK is clinically important because of its relationship to drug resistance and sensitivity. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0214 (3256/152224) while in subpopulation NFE AF= 0.0342 (2322/67976). AF 95% confidence interval is 0.033. There are 55 homozygotes in gnomad4. There are 1511 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 55 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DCK | NM_000788.3 | c.*1248A>G | 3_prime_UTR_variant | 7/7 | ENST00000286648.10 | ||
DCK | XM_047449689.1 | c.*1248A>G | 3_prime_UTR_variant | 7/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DCK | ENST00000286648.10 | c.*1248A>G | 3_prime_UTR_variant | 7/7 | 1 | NM_000788.3 | P1 | ||
DCK | ENST00000504730.5 | c.*1315A>G | 3_prime_UTR_variant | 6/6 | 3 | ||||
DCK | ENST00000504952.1 | c.*1174A>G | 3_prime_UTR_variant | 8/8 | 3 | ||||
DCK | ENST00000503359.5 | c.*1975A>G | 3_prime_UTR_variant, NMD_transcript_variant | 7/7 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0214 AC: 3256AN: 152106Hom.: 55 Cov.: 33
GnomAD3 genomes
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GnomAD4 exome Data not reliable, filtered out with message: AC0AC: 0AN: 0Hom.: 0 Cov.: 0AC XY: 0AN XY: 0
GnomAD4 exome
Data not reliable, filtered out with message: AC0
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GnomAD4 genome ? AF: 0.0214 AC: 3256AN: 152224Hom.: 55 Cov.: 33 AF XY: 0.0203 AC XY: 1511AN XY: 74440
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?
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3444
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at