Genetic Variant CDA:p.Thr145Thr (chr1-20618562-C-T) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001785.3(CDA):c.435C>T(p.Thr145Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 1,580,002 control chromosomes in the GnomAD database, including 81,410 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 0.33 ( 8558 hom., cov: 30)

Exomes 𝑓: 0.32 ( 72852 hom. )

Consequence

CDA
NM_001785.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.12

Publications

70 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 -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.75).

BP7

Synonymous conserved (PhyloP=1.12 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.38 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDA	NM_001785.3 link	c.435C>T	p.Thr145Thr	synonymous_variant	Exon 4 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.435C>T	p.Thr145Thr	synonymous_variant	Exon 4 of 4	1	NM_001785.3	ENSP00000364212.3		P32320
CDA	ENST00000461985.1 link	n.421C>T		non_coding_transcript_exon_variant	Exon 3 of 3	3

Frequencies

GnomAD3 genomes

AF:

0.333

AC:

50510

AN:

151562

Hom.:

8544

Cov.:

show subpopulations

Gnomad AFR

AF:

0.385

Gnomad AMI

AF:

0.428

Gnomad AMR

AF:

0.332

Gnomad ASJ

AF:

0.239

Gnomad EAS

AF:

0.257

Gnomad SAS

AF:

0.261

Gnomad FIN

AF:

0.314

Gnomad MID

AF:

0.264

Gnomad NFE

AF:

0.320

Gnomad OTH

AF:

0.316

GnomAD2 exomes

AF:

0.307

AC:

76987

AN:

250834

AF XY:

0.304

show subpopulations

Gnomad AFR exome

AF:

0.389

Gnomad AMR exome

AF:

0.308

Gnomad ASJ exome

AF:

0.241

Gnomad EAS exome

AF:

0.237

Gnomad FIN exome

AF:

0.322

Gnomad NFE exome

AF:

0.321

Gnomad OTH exome

AF:

0.302

GnomAD4 exome

AF:

0.317

AC:

452357

AN:

1428322

Hom.:

72852

Cov.:

AF XY:

0.315

AC XY:

224241

AN XY:

712566

show subpopulations

African (AFR)

AF:

0.382

AC:

12483

AN:

32718

American (AMR)

AF:

0.311

AC:

13864

AN:

44640

Ashkenazi Jewish (ASJ)

AF:

0.241

AC:

6256

AN:

25918

East Asian (EAS)

AF:

0.267

AC:

10546

AN:

39492

South Asian (SAS)

AF:

0.268

AC:

22903

AN:

85598

European-Finnish (FIN)

AF:

0.319

AC:

16975

AN:

53292

Middle Eastern (MID)

AF:

0.235

AC:

1345

AN:

5718

European-Non Finnish (NFE)

AF:

0.323

AC:

349548

AN:

1081728

Other (OTH)

AF:

0.311

AC:

18437

AN:

59218

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.447

Heterozygous variant carriers

14902

29804

44705

59607

74509

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

11224

22448

33672

44896

56120

<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:

0.333

AC:

50559

AN:

151680

Hom.:

8558

Cov.:

AF XY:

0.331

AC XY:

24522

AN XY:

74110

show subpopulations

African (AFR)

AF:

0.385

AC:

15920

AN:

41366

American (AMR)

AF:

0.333

AC:

5069

AN:

15240

Ashkenazi Jewish (ASJ)

AF:

0.239

AC:

829

AN:

3470

East Asian (EAS)

AF:

0.258

AC:

1319

AN:

5104

South Asian (SAS)

AF:

0.261

AC:

1253

AN:

4804

European-Finnish (FIN)

AF:

0.314

AC:

3312

AN:

10548

Middle Eastern (MID)

AF:

0.265

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.320

AC:

21732

AN:

67844

Other (OTH)

AF:

0.313

AC:

658

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.473

Heterozygous variant carriers

1500

2999

4499

5998

7498

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

496

992

1488

1984

2480

<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:

0.326

Hom.:

24261

Bravo

AF:

0.338

Asia WGS

AF:

0.260

AC:

905

AN:

3478

EpiCase

AF:

0.313

EpiControl

AF:

0.314

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

1.5

(source)

DANN

Benign

0.42

PhyloP100

1.1

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