rs4655226

Variant names:

• chr1-20601791-C-T
• rs4655226
• NM_001785.3:c.155-3137C>T

Variant summary

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

The NM_001785.3(CDA):​c.155-3137C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 152,068 control chromosomes in the GnomAD database, including 1,369 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 0.13 (1369 hom., cov: 30)
• Consequence: CDA NM_001785.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0980

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=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDA	NM_001785.3	c.155-3137C>T		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.155-3137C>T		intron_variant	Intron 1 of 3	1	NM_001785.3	ENSP00000364212.3
CDA	ENST00000461985.1	n.199-3137C>T		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20031 AN: 151950 Hom.: 1358 Cov.: 30

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.0971

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.0869

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.132 AC: 20066 AN: 152068 Hom.: 1369 Cov.: 30 AF XY: 0.131 AC XY: 9717 AN XY: 74316

Gnomad4 AFR AF: 0.141

Gnomad4 AMR AF: 0.173

Gnomad4 ASJ AF: 0.0971

Gnomad4 EAS AF: 0.169

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.0869

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.126

Alfa AF: 0.126 Hom.: 2187

Bravo AF: 0.137

Asia WGS AF: 0.154 AC: 534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.2
DANN	Benign	0.78

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: rs4655226; hg19: chr1-20928284;