1-20605335-A-T

Variant names:

• chr1-20605335-A-T
• rs818194
• NM_001785.3:c.266+296A>T

Variant summary

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

The NM_001785.3(CDA):​c.266+296A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.721 in 151,720 control chromosomes in the GnomAD database, including 40,279 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 0.72 (40279 hom., cov: 29)
• Consequence: CDA NM_001785.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.264
• Publications: 5 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.802 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDA	NM_001785.3	c.266+296A>T		intron_variant	Intron 2 of 3	ENST00000375071.4	NP_001776.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDA	ENST00000375071.4	c.266+296A>T		intron_variant	Intron 2 of 3	1	NM_001785.3	ENSP00000364212.3
CDA	ENST00000461985.1	n.310+296A>T		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.721 AC: 109318 AN: 151602 Hom.: 40263 Cov.: 29

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.708

Gnomad AMR AF: 0.739

Gnomad ASJ AF: 0.847

Gnomad EAS AF: 0.805

Gnomad SAS AF: 0.823

Gnomad FIN AF: 0.809

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.785

Gnomad OTH AF: 0.738

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

GnomAD4 genome AF: 0.721 AC: 109371 AN: 151720 Hom.: 40279 Cov.: 29 AF XY: 0.725 AC XY: 53731 AN XY: 74142

African (AFR) AF: 0.551 AC: 22774 AN: 41304

American (AMR) AF: 0.739 AC: 11271 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.847 AC: 2940 AN: 3470

East Asian (EAS) AF: 0.805 AC: 4146 AN: 5150

South Asian (SAS) AF: 0.823 AC: 3949 AN: 4796

European-Finnish (FIN) AF: 0.809 AC: 8517 AN: 10524

Middle Eastern (MID) AF: 0.776 AC: 228 AN: 294

European-Non Finnish (NFE) AF: 0.785 AC: 53345 AN: 67916

Other (OTH) AF: 0.741 AC: 1560 AN: 2106

Alfa AF: 0.689 Hom.: 2194

Bravo AF: 0.709

Asia WGS AF: 0.789 AC: 2744 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	3.8
DANN	Benign	0.59
PhyloP100		0.26
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: rs818194; hg19: chr1-20931828;