chr4-70993963-G-A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_000788.3(DCK):​c.91+37G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000683 in 1,317,338 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
Exomes 𝑓: 0.0000068 ( 0 hom. )

Consequence

DCK
NM_000788.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.389

Publications

4 publications found
Variant links:
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: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.75).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
DCKNM_000788.3 linkc.91+37G>A intron_variant Intron 1 of 6 ENST00000286648.10 NP_000779.1 P27707F5CTF3
DCKXM_047449689.1 linkc.-180G>A 5_prime_UTR_variant Exon 1 of 7 XP_047305645.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
DCKENST00000286648.10 linkc.91+37G>A intron_variant Intron 1 of 6 1 NM_000788.3 ENSP00000286648.5 P27707

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD2 exomes
AF:
0.00000426
AC:
1
AN:
234998
AF XY:
0.00000787
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00000951
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000683
AC:
9
AN:
1317338
Hom.:
0
Cov.:
19
AF XY:
0.00000604
AC XY:
4
AN XY:
662248
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
30570
American (AMR)
AF:
0.00
AC:
0
AN:
43370
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
25054
East Asian (EAS)
AF:
0.00
AC:
0
AN:
38816
South Asian (SAS)
AF:
0.00
AC:
0
AN:
82400
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
52604
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5492
European-Non Finnish (NFE)
AF:
0.00000814
AC:
8
AN:
983256
Other (OTH)
AF:
0.0000179
AC:
1
AN:
55776
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.536
Heterozygous variant carriers
0
1
2
2
3
4
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
Cov.:
32
Alfa
AF:
0.00
Hom.:
6
Bravo
AF:
0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.75
CADD
Benign
4.8
DANN
Benign
0.88
PhyloP100
0.39
PromoterAI
-0.14
Neutral

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.070
Details are displayed if max score is > 0.2

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

Publications

Other links and lift over

dbSNP: rs9997790; hg19: chr4-71859680; API