1-20590713-G-A

Position:

• chr1-20590713-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001785.3(CDA):​c.154+1430G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 152,152 control chromosomes in the GnomAD database, including 5,477 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 0.24 (5477 hom., cov: 32)
• Consequence: CDA NM_001785.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.126

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.322 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDA	NM_001785.3	c.154+1430G>A		intron_variant		ENST00000375071.4	NP_001776.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDA	ENST00000375071.4	c.154+1430G>A		intron_variant		1	NM_001785.3	ENSP00000364212	P1
CDA	ENST00000461985.1	n.198+1430G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37233 AN: 152034 Hom.: 5473 Cov.: 32

Gnomad AFR AF: 0.0942

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.245 AC: 37240 AN: 152152 Hom.: 5477 Cov.: 32 AF XY: 0.241 AC XY: 17929 AN XY: 74372

Gnomad4 AFR AF: 0.0941

Gnomad4 AMR AF: 0.313

Gnomad4 ASJ AF: 0.397

Gnomad4 EAS AF: 0.143

Gnomad4 SAS AF: 0.206

Gnomad4 FIN AF: 0.214

Gnomad4 NFE AF: 0.326

Gnomad4 OTH AF: 0.277

Alfa AF: 0.324 Hom.: 16922

Bravo AF: 0.246

Asia WGS AF: 0.189 AC: 657 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.6
DANN	Benign	0.85

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: rs471760; hg19: chr1-20917206;