1-20616702-A-G

Variant names:

• chr1-20616702-A-G
• rs12404655
• NM_001785.3:c.325-1750A>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.325-1750A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 151,884 control chromosomes in the GnomAD database, including 2,943 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 0.19 (2943 hom., cov: 32)
• Consequence: CDA NM_001785.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.126
• Publications: 16 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=-0.67).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.232 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDA	NM_001785.3	c.325-1750A>G		intron_variant	Intron 3 of 3	ENST00000375071.4	NP_001776.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDA	ENST00000375071.4	c.325-1750A>G		intron_variant	Intron 3 of 3	1	NM_001785.3	ENSP00000364212.3
CDA	ENST00000461985.1	n.311-1750A>G		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28193 AN: 151778 Hom.: 2939 Cov.: 32

Gnomad AFR AF: 0.0892

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.186 AC: 28194 AN: 151884 Hom.: 2943 Cov.: 32 AF XY: 0.184 AC XY: 13624 AN XY: 74236

African (AFR) AF: 0.0891 AC: 3682 AN: 41324

American (AMR) AF: 0.183 AC: 2791 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 863 AN: 3466

East Asian (EAS) AF: 0.141 AC: 731 AN: 5172

South Asian (SAS) AF: 0.178 AC: 857 AN: 4820

European-Finnish (FIN) AF: 0.240 AC: 2537 AN: 10564

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.235 AC: 16002 AN: 67986

Other (OTH) AF: 0.212 AC: 446 AN: 2104

Alfa AF: 0.222 Hom.: 6603

Bravo AF: 0.180

Asia WGS AF: 0.150 AC: 522 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	11
DANN	Benign	0.78
PhyloP100		-0.13
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: rs12404655; hg19: chr1-20943195;