chr1-20589096-TC-T

Position:

• chr1-20589096-TC-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001785.3(CDA):​c.-31del 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.513

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
CDA	NM_001785.3	c.-31del		5_prime_UTR_variant	1/4	ENST00000375071.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDA	ENST00000375071.4	c.-31del		5_prime_UTR_variant	1/4	1	NM_001785.3	P1
CDA	ENST00000461985.1	n.14del		non_coding_transcript_exon_variant	1/3	3

Frequencies

GnomAD3 genomes AF: 0.562 AC: 85348 AN: 151858 Hom.: 24076 Cov.: 0

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

GnomAD3 exomes AF: 0.536 AC: 134252 AN: 250688 Hom.: 36348 AF XY: 0.538 AC XY: 72960 AN XY: 135642

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 SAS exome AF: 0.523

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.: 0 AF XY: 0.550 AC XY: 399894 AN XY: 726872

Gnomad4 AFR exome AF: 0.625

Gnomad4 AMR exome AF: 0.469

Gnomad4 ASJ exome AF: 0.610

Gnomad4 EAS exome AF: 0.442

Gnomad4 SAS exome AF: 0.524

Gnomad4 FIN exome AF: 0.536

Gnomad4 NFE exome AF: 0.557

Gnomad4 OTH exome AF: 0.558

GnomAD4 genome AF: 0.562 AC: 85424 AN: 151976 Hom.: 24109 Cov.: 0 AF XY: 0.559 AC XY: 41536 AN XY: 74276

Gnomad4 AFR AF: 0.618

Gnomad4 AMR AF: 0.526

Gnomad4 ASJ AF: 0.605

Gnomad4 EAS AF: 0.440

Gnomad4 SAS AF: 0.520

Gnomad4 FIN AF: 0.535

Gnomad4 NFE AF: 0.549

Gnomad4 OTH AF: 0.568

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

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

LitVar

Other links and lift over

dbSNP: rs3215400; hg19: chr1-20915589;