1-20590298-A-G

Variant names:

• chr1-20590298-A-G
• rs818202
• NM_001785.3:c.154+1015A>G

Variant summary

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

The NM_001785.3(CDA):​c.154+1015A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.54 in 152,004 control chromosomes in the GnomAD database, including 22,881 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 0.54 (22881 hom., cov: 32)
• Consequence: CDA NM_001785.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.729
• Publications: 13 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.602 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDA	NM_001785.3	c.154+1015A>G		intron_variant	Intron 1 of 3	ENST00000375071.4	NP_001776.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDA	ENST00000375071.4	c.154+1015A>G		intron_variant	Intron 1 of 3	1	NM_001785.3	ENSP00000364212.3
CDA	ENST00000461985.1	n.198+1015A>G		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.540 AC: 82088 AN: 151886 Hom.: 22857 Cov.: 32

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.770

Gnomad AMR AF: 0.555

Gnomad ASJ AF: 0.624

Gnomad EAS AF: 0.309

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.608

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.556

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

GnomAD4 genome AF: 0.540 AC: 82156 AN: 152004 Hom.: 22881 Cov.: 32 AF XY: 0.536 AC XY: 39867 AN XY: 74318

African (AFR) AF: 0.433 AC: 17944 AN: 41426

American (AMR) AF: 0.556 AC: 8486 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.624 AC: 2165 AN: 3470

East Asian (EAS) AF: 0.310 AC: 1600 AN: 5162

South Asian (SAS) AF: 0.464 AC: 2239 AN: 4822

European-Finnish (FIN) AF: 0.608 AC: 6419 AN: 10562

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.607 AC: 41258 AN: 67968

Other (OTH) AF: 0.551 AC: 1164 AN: 2112

Alfa AF: 0.584 Hom.: 108768

Bravo AF: 0.532

Asia WGS AF: 0.390 AC: 1359 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.55
DANN	Benign	0.40
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: rs818202; hg19: chr1-20916791;