Genetic Variant NM_016308.3:c.*2047G>A (chr1-47378792-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_016308.3(CMPK1):c.*2047G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.395 in 152,096 control chromosomes in the GnomAD database, including 14,711 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 0.39 ( 14711 hom., cov: 32)

Exomes 𝑓: 0.50 ( 0 hom. )

Consequence

CMPK1
NM_016308.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0110

Publications

10 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]

CMPK1 links:

Genome browser will be placed here

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=-0.75).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.523 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
CMPK1	NM_016308.3 link	c.*2047G>A	3_prime_UTR_variant	Exon 6 of 6	ENST00000371873.10	NP_057392.1	P30085-3
CMPK1	NR_046394.2 link	n.2813G>A	non_coding_transcript_exon_variant	Exon 5 of 5
CMPK1	NM_001366135.1 link	c.*2047G>A	3_prime_UTR_variant	Exon 6 of 6		NP_001353064.1
CMPK1	NM_001136140.2 link	c.*2047G>A	3_prime_UTR_variant	Exon 5 of 5		NP_001129612.1	P30085A0A494BXC7

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
CMPK1	ENST00000371873.10 link	c.*2047G>A	3_prime_UTR_variant	Exon 6 of 6	1	NM_016308.3	ENSP00000360939.5	P30085-3
CMPK1	ENST00000699075.1 link	c.*2047G>A	3_prime_UTR_variant	Exon 6 of 6			ENSP00000514114.1	P30085-1
CMPK1	ENST00000699074.1 link	c.549+3499G>A	intron_variant	Intron 5 of 5			ENSP00000514113.1	A0A8V8TMN5

Frequencies

GnomAD3 genomes

AF:

0.395

AC:

60016

AN:

151976

Hom.:

14707

Cov.:

show subpopulations

Gnomad AFR

AF:

0.105

Gnomad AMI

AF:

0.512

Gnomad AMR

AF:

0.418

Gnomad ASJ

AF:

0.638

Gnomad EAS

AF:

0.208

Gnomad SAS

AF:

0.451

Gnomad FIN

AF:

0.613

Gnomad MID

AF:

0.475

Gnomad NFE

AF:

0.527

Gnomad OTH

AF:

0.432

GnomAD4 exome

AF:

0.500

AC:

AN:

Hom.:

Cov.:

AF XY:

0.500

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.395

AC:

60023

AN:

152094

Hom.:

14711

Cov.:

AF XY:

0.397

AC XY:

29543

AN XY:

74336

show subpopulations

African (AFR)

AF:

0.105

AC:

4348

AN:

41502

American (AMR)

AF:

0.418

AC:

6384

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.638

AC:

2216

AN:

3472

East Asian (EAS)

AF:

0.208

AC:

1079

AN:

5184

South Asian (SAS)

AF:

0.453

AC:

2183

AN:

4818

European-Finnish (FIN)

AF:

0.613

AC:

6469

AN:

10556

Middle Eastern (MID)

AF:

0.490

AC:

144

AN:

294

European-Non Finnish (NFE)

AF:

0.527

AC:

35817

AN:

67952

Other (OTH)

AF:

0.433

AC:

916

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1616

3233

4849

6466

8082

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

560

1120

1680

2240

2800

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.476

Hom.:

49396

Bravo

AF:

0.365

Asia WGS

AF:

0.320

AC:

1110

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

3.5

(source)

DANN

Benign

0.64

PhyloP100

-0.011

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over