Genetic Variant NM_016308.3:c.*360C>T (chr1-47377105-C-T) – 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.*360C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.399 in 163,658 control chromosomes in the GnomAD database, including 16,157 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 ( 14665 hom., cov: 32)

Exomes 𝑓: 0.49 ( 1492 hom. )

Consequence

CMPK1
NM_016308.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.244

Publications

17 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=-0.84).

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.*360C>T	3_prime_UTR_variant	Exon 6 of 6	ENST00000371873.10	NP_057392.1	P30085-3
CMPK1	NR_046394.2 link	n.1126C>T	non_coding_transcript_exon_variant	Exon 5 of 5
CMPK1	NM_001366135.1 link	c.*360C>T	3_prime_UTR_variant	Exon 6 of 6		NP_001353064.1
CMPK1	NM_001136140.2 link	c.*360C>T	3_prime_UTR_variant	Exon 5 of 5		NP_001129612.1	P30085A0A494BXC7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CMPK1	ENST00000371873.10 link	c.*360C>T		3_prime_UTR_variant	Exon 6 of 6	1	NM_016308.3	ENSP00000360939.5		P30085-3

Frequencies

GnomAD3 genomes

AF:

0.393

AC:

59630

AN:

151850

Hom.:

14661

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0966

Gnomad AMI

AF:

0.514

Gnomad AMR

AF:

0.418

Gnomad ASJ

AF:

0.639

Gnomad EAS

AF:

0.209

Gnomad SAS

AF:

0.451

Gnomad FIN

AF:

0.613

Gnomad MID

AF:

0.478

Gnomad NFE

AF:

0.527

Gnomad OTH

AF:

0.434

GnomAD4 exome

AF:

0.490

AC:

5731

AN:

11690

Hom.:

1492

Cov.:

AF XY:

0.494

AC XY:

2951

AN XY:

5976

show subpopulations

African (AFR)

AF:

0.0997

AC:

AN:

612

American (AMR)

AF:

0.411

AC:

138

AN:

336

Ashkenazi Jewish (ASJ)

AF:

0.605

AC:

306

AN:

506

East Asian (EAS)

AF:

0.245

AC:

205

AN:

838

South Asian (SAS)

AF:

0.432

AC:

AN:

European-Finnish (FIN)

AF:

0.601

AC:

460

AN:

766

Middle Eastern (MID)

AF:

0.636

AC:

AN:

European-Non Finnish (NFE)

AF:

0.533

AC:

4067

AN:

7628

Other (OTH)

AF:

0.487

AC:

414

AN:

850

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

149

298

446

595

744

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

100

<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

AF:

0.392

AC:

59631

AN:

151968

Hom.:

14665

Cov.:

AF XY:

0.395

AC XY:

29337

AN XY:

74258

show subpopulations

African (AFR)

AF:

0.0963

AC:

3995

AN:

41466

American (AMR)

AF:

0.417

AC:

6363

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.639

AC:

2216

AN:

3470

East Asian (EAS)

AF:

0.208

AC:

1079

AN:

5176

South Asian (SAS)

AF:

0.453

AC:

2182

AN:

4820

European-Finnish (FIN)

AF:

0.613

AC:

6460

AN:

10532

Middle Eastern (MID)

AF:

0.493

AC:

144

AN:

292

European-Non Finnish (NFE)

AF:

0.527

AC:

35807

AN:

67926

Other (OTH)

AF:

0.435

AC:

918

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1590

3180

4769

6359

7949

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

556

1112

1668

2224

2780

<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.:

45755

Bravo

AF:

0.363

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

6.2

(source)

DANN

Benign

0.68

PhyloP100

-0.24

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over