chr1-20597767-G-A

Position:

• chr1-20597767-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.155-7161G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.352 in 152,048 control chromosomes in the GnomAD database, including 9,773 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 0.35 (9773 hom., cov: 32)
• Consequence: CDA NM_001785.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.321

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDA	NM_001785.3	c.155-7161G>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.155-7161G>A		intron_variant		1	NM_001785.3	ENSP00000364212	P1
CDA	ENST00000461985.1	n.199-7161G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.352 AC: 53536 AN: 151930 Hom.: 9762 Cov.: 32

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.352 AC: 53561 AN: 152048 Hom.: 9773 Cov.: 32 AF XY: 0.353 AC XY: 26227 AN XY: 74322

Gnomad4 AFR AF: 0.248

Gnomad4 AMR AF: 0.425

Gnomad4 ASJ AF: 0.454

Gnomad4 EAS AF: 0.448

Gnomad4 SAS AF: 0.355

Gnomad4 FIN AF: 0.310

Gnomad4 NFE AF: 0.392

Gnomad4 OTH AF: 0.382

Alfa AF: 0.388 Hom.: 7188

Bravo AF: 0.357

Asia WGS AF: 0.401 AC: 1396 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.46

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: rs818199; hg19: chr1-20924260;