rs4655226

Variant names:

• chr1-20601791-C-T
• rs4655226
• NM_001785.3:c.155-3137C>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.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
• Publications: 12 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001785.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDA	NM_001785.3	MANE Select	c.155-3137C>T		intron	N/A	NP_001776.1	P32320

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDA	ENST00000375071.4	TSL:1 MANE Select	c.155-3137C>T		intron	N/A	ENSP00000364212.3	P32320
	CDA	ENST00000904801.1		c.155-3137C>T		intron	N/A	ENSP00000574860.1
	CDA	ENST00000916580.1		c.155-3107C>T		intron	N/A	ENSP00000586639.1

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

African (AFR) AF: 0.141 AC: 5844 AN: 41470

American (AMR) AF: 0.173 AC: 2638 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0971 AC: 337 AN: 3472

East Asian (EAS) AF: 0.169 AC: 871 AN: 5160

South Asian (SAS) AF: 0.113 AC: 546 AN: 4818

European-Finnish (FIN) AF: 0.0869 AC: 918 AN: 10568

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.125 AC: 8472 AN: 67978

Other (OTH) AF: 0.126 AC: 266 AN: 2108

Alfa AF: 0.129 Hom.: 5391

Bravo AF: 0.137

Asia WGS AF: 0.154 AC: 534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.2
DANN	Benign	0.78
PhyloP100		-0.098
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: rs4655226; hg19: chr1-20928284;