Genetic Variant CDA:c.-31delC (chr1-20589096-TC-T) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_001785.3(CDA):c.-31delC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.56 ( 24109 hom., cov: 0)

Exomes 𝑓: 0.55 ( 223019 hom. )

Consequence

CDA
NM_001785.3 5_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.513

Publications

33 publications found

Variant links:

Genes affected

CDA (HGNC:1712): (cytidine deaminase) This gene encodes an enzyme involved in pyrimidine salvaging. The encoded protein forms a homotetramer that catalyzes the irreversible hydrolytic deamination of cytidine and deoxycytidine to uridine and deoxyuridine, respectively. It is one of several deaminases responsible for maintaining the cellular pyrimidine pool. Mutations in this gene are associated with decreased sensitivity to the cytosine nucleoside analogue cytosine arabinoside used in the treatment of certain childhood leukemias. [provided by RefSeq, Jul 2008]

CDA links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.612 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDA	NM_001785.3 link	c.-31delC		5_prime_UTR_variant	Exon 1 of 4	ENST00000375071.4	NP_001776.1	P32320

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDA	ENST00000375071.4 link	c.-31delC		5_prime_UTR_variant	Exon 1 of 4	1	NM_001785.3	ENSP00000364212.3		P32320
CDA	ENST00000461985.1 link	n.14delC		non_coding_transcript_exon_variant	Exon 1 of 3	3

Frequencies

GnomAD3 genomes

AF:

0.562

AC:

85348

AN:

151858

Hom.:

24076

Cov.:

show subpopulations

Gnomad AFR

AF:

0.618

Gnomad AMI

AF:

0.649

Gnomad AMR

AF:

0.525

Gnomad ASJ

AF:

0.605

Gnomad EAS

AF:

0.439

Gnomad SAS

AF:

0.519

Gnomad FIN

AF:

0.535

Gnomad MID

AF:

0.611

Gnomad NFE

AF:

0.549

Gnomad OTH

AF:

0.576

GnomAD2 exomes

AF:

0.536

AC:

134252

AN:

250688

AF XY:

0.538

show subpopulations

Gnomad AFR exome

AF:

0.623

Gnomad AMR exome

AF:

0.460

Gnomad ASJ exome

AF:

0.607

Gnomad EAS exome

AF:

0.423

Gnomad FIN exome

AF:

0.539

Gnomad NFE exome

AF:

0.560

Gnomad OTH exome

AF:

0.550

GnomAD4 exome

AF:

0.551

AC:

805536

AN:

1461072

Hom.:

223019

Cov.:

AF XY:

0.550

AC XY:

399894

AN XY:

726872

show subpopulations

African (AFR)

AF:

0.625

AC:

20913

AN:

33472

American (AMR)

AF:

0.469

AC:

20951

AN:

44712

Ashkenazi Jewish (ASJ)

AF:

0.610

AC:

15929

AN:

26130

East Asian (EAS)

AF:

0.442

AC:

17525

AN:

39694

South Asian (SAS)

AF:

0.524

AC:

45161

AN:

86244

European-Finnish (FIN)

AF:

0.536

AC:

28485

AN:

53156

Middle Eastern (MID)

AF:

0.608

AC:

3500

AN:

5752

European-Non Finnish (NFE)

AF:

0.557

AC:

619365

AN:

1111534

Other (OTH)

AF:

0.558

AC:

33707

AN:

60378

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.485

Heterozygous variant carriers

19802

39604

59406

79208

99010

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.562

AC:

85424

AN:

151976

Hom.:

24109

Cov.:

AF XY:

0.559

AC XY:

41536

AN XY:

74276

show subpopulations

African (AFR)

AF:

0.618

AC:

25632

AN:

41456

American (AMR)

AF:

0.526

AC:

8024

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.605

AC:

2097

AN:

3466

East Asian (EAS)

AF:

0.440

AC:

2267

AN:

5156

South Asian (SAS)

AF:

0.520

AC:

2509

AN:

4826

European-Finnish (FIN)

AF:

0.535

AC:

5649

AN:

10556

Middle Eastern (MID)

AF:

0.619

AC:

182

AN:

294

European-Non Finnish (NFE)

AF:

0.549

AC:

37275

AN:

67938

Other (OTH)

AF:

0.568

AC:

1198

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1901

3801

5702

7602

9503

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.562

Hom.:

4380

Bravo

AF:

0.564

Asia WGS

AF:

0.482

AC:

1678

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.51

Mutation Taster

=299/1

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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1-20589096-TCC-TC

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