4-70993963-G-C
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_000788.3(DCK):c.91+37G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0163 in 1,469,492 control chromosomes in the GnomAD database, including 253 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 0.014 ( 23 hom., cov: 32)
Exomes 𝑓: 0.017 ( 230 hom. )
Consequence
DCK
NM_000788.3 intron
NM_000788.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.389
Publications
4 publications found
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]
MOB1B (HGNC:29801): (MOB kinase activator 1B) The protein encoded by this gene is similar to the yeast Mob1 protein. Yeast Mob1 binds Mps1p, a protein kinase essential for spindle pole body duplication and mitotic checkpoint regulation. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BS1
Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0142 (2165/152340) while in subpopulation NFE AF = 0.0197 (1343/68022). AF 95% confidence interval is 0.0189. There are 23 homozygotes in GnomAd4. There are 1068 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
BS2
High Homozygotes in GnomAd4 at 23 gene
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0142 AC: 2165AN: 152224Hom.: 23 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
2165
AN:
152224
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD2 exomes AF: 0.0147 AC: 3445AN: 234998 AF XY: 0.0150 show subpopulations
GnomAD2 exomes
AF:
AC:
3445
AN:
234998
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0166 AC: 21845AN: 1317152Hom.: 230 Cov.: 19 AF XY: 0.0164 AC XY: 10859AN XY: 662174 show subpopulations
GnomAD4 exome
AF:
AC:
21845
AN:
1317152
Hom.:
Cov.:
19
AF XY:
AC XY:
10859
AN XY:
662174
show subpopulations
African (AFR)
AF:
AC:
104
AN:
30570
American (AMR)
AF:
AC:
441
AN:
43368
Ashkenazi Jewish (ASJ)
AF:
AC:
523
AN:
25052
East Asian (EAS)
AF:
AC:
3
AN:
38818
South Asian (SAS)
AF:
AC:
599
AN:
82398
European-Finnish (FIN)
AF:
AC:
1101
AN:
52604
Middle Eastern (MID)
AF:
AC:
244
AN:
5492
European-Non Finnish (NFE)
AF:
AC:
17949
AN:
983082
Other (OTH)
AF:
AC:
881
AN:
55768
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1105
2210
3316
4421
5526
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome AF: 0.0142 AC: 2165AN: 152340Hom.: 23 Cov.: 32 AF XY: 0.0143 AC XY: 1068AN XY: 74496 show subpopulations
GnomAD4 genome
AF:
AC:
2165
AN:
152340
Hom.:
Cov.:
32
AF XY:
AC XY:
1068
AN XY:
74496
show subpopulations
African (AFR)
AF:
AC:
165
AN:
41586
American (AMR)
AF:
AC:
217
AN:
15308
Ashkenazi Jewish (ASJ)
AF:
AC:
81
AN:
3472
East Asian (EAS)
AF:
AC:
2
AN:
5176
South Asian (SAS)
AF:
AC:
37
AN:
4832
European-Finnish (FIN)
AF:
AC:
218
AN:
10622
Middle Eastern (MID)
AF:
AC:
14
AN:
294
European-Non Finnish (NFE)
AF:
AC:
1343
AN:
68022
Other (OTH)
AF:
AC:
39
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.506
Heterozygous variant carriers
0
106
213
319
426
532
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
10
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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