rs7543016

Variant summary

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

The NM_016308.3(CMPK1):​c.22G>A​(p.Gly8Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000447 in 1,342,244 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict 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: 31)
Exomes 𝑓: 0.0000045 ( 0 hom. )

Consequence

CMPK1
NM_016308.3 missense

Scores

2
14

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0490

Publications

39 publications found
Variant links:
Genes affected
CMPK1 (HGNC:18170): (cytidine/uridine monophosphate kinase 1) This gene encodes one of the enzymes required for cellular nucleic acid biosynthesis. This enzyme catalyzes the transfer of a phosphate group from ATP to CMP, UMP, or dCMP, to form the corresponding diphosphate nucleotide. Alternate splicing results in both coding and non-coding transcript variants. [provided by RefSeq, Feb 2012]

Genome browser will be placed here

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 (MetaRNN=0.04375282).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CMPK1NM_016308.3 linkc.22G>A p.Gly8Arg missense_variant Exon 1 of 6 ENST00000371873.10 NP_057392.1 P30085-3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CMPK1ENST00000371873.10 linkc.22G>A p.Gly8Arg missense_variant Exon 1 of 6 1 NM_016308.3 ENSP00000360939.5 P30085-3

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD2 exomes
AF:
0.00
AC:
0
AN:
150196
AF XY:
0.00
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:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000447
AC:
6
AN:
1342244
Hom.:
0
Cov.:
37
AF XY:
0.00000451
AC XY:
3
AN XY:
665760
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
27766
American (AMR)
AF:
0.00
AC:
0
AN:
34724
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
22920
East Asian (EAS)
AF:
0.00
AC:
0
AN:
30804
South Asian (SAS)
AF:
0.0000271
AC:
2
AN:
73900
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
47458
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
3770
European-Non Finnish (NFE)
AF:
0.00000382
AC:
4
AN:
1046872
Other (OTH)
AF:
0.00
AC:
0
AN:
54030
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.558
Heterozygous variant carriers
0
1
1
2
2
3
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.:
31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
-0.25
T
BayesDel_noAF
Benign
-0.60
CADD
Benign
6.0
DANN
Benign
0.93
Eigen
Benign
-1.3
Eigen_PC
Benign
-1.2
FATHMM_MKL
Benign
0.067
N
LIST_S2
Benign
0.16
T;T;T
M_CAP
Uncertain
0.20
D
MetaRNN
Benign
0.044
T;T;T
MetaSVM
Benign
-0.92
T
PhyloP100
0.049
PrimateAI
Uncertain
0.59
T
PROVEAN
Benign
0.16
N;N;N
REVEL
Benign
0.056
Sift
Benign
1.0
T;T;T
Sift4G
Benign
0.72
T;T;T
Vest4
0.23
MutPred
0.36
Gain of MoRF binding (P = 0.0023);Gain of MoRF binding (P = 0.0023);Gain of MoRF binding (P = 0.0023);
MVP
0.15
MPC
1.2
ClinPred
0.37
T
GERP RS
2.9
PromoterAI
0.027
Neutral
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
gMVP
0.30
Mutation Taster
=97/3
polymorphism

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

Other links and lift over

dbSNP: rs7543016; hg19: chr1-47799639; API