rs572529

Variant names:

• chr1-20609683-C-T
• rs572529
• NM_001785.3:c.267-4159C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001785.3(CDA):​c.267-4159C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.34 in 152,000 control chromosomes in the GnomAD database, including 8,928 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 0.34 (8928 hom., cov: 32)
• Consequence: CDA NM_001785.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.733
• Publications: 7 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDA	NM_001785.3	c.267-4159C>T		intron_variant	Intron 2 of 3	ENST00000375071.4	NP_001776.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDA	ENST00000375071.4	c.267-4159C>T		intron_variant	Intron 2 of 3	1	NM_001785.3	ENSP00000364212.3
CDA	ENST00000461985.1	n.310+4644C>T		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.340 AC: 51599 AN: 151882 Hom.: 8923 Cov.: 32

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.401

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.361

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.340 AC: 51615 AN: 152000 Hom.: 8928 Cov.: 32 AF XY: 0.339 AC XY: 25151 AN XY: 74264

African (AFR) AF: 0.277 AC: 11499 AN: 41482

American (AMR) AF: 0.400 AC: 6121 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.425 AC: 1474 AN: 3470

East Asian (EAS) AF: 0.279 AC: 1442 AN: 5162

South Asian (SAS) AF: 0.276 AC: 1333 AN: 4822

European-Finnish (FIN) AF: 0.311 AC: 3269 AN: 10520

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.372 AC: 25291 AN: 67948

Other (OTH) AF: 0.358 AC: 758 AN: 2116

Alfa AF: 0.350 Hom.: 3818

Bravo AF: 0.344

Asia WGS AF: 0.295 AC: 1027 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.0
DANN	Benign	0.73
PhyloP100		0.73
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs572529; hg19: chr1-20936176;