1-20608303-A-G

Variant names:

• chr1-20608303-A-G
• rs1689924
• NM_001785.3:c.266+3264A>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.266+3264A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.501 in 152,024 control chromosomes in the GnomAD database, including 19,118 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 0.50 (19118 hom., cov: 32)
• Consequence: CDA NM_001785.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 11 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.507 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.266+3264A>G		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.266+3264A>G		intron	N/A	ENSP00000364212.3	P32320
	CDA	ENST00000904801.1		c.266+3264A>G		intron	N/A	ENSP00000574860.1
	CDA	ENST00000916580.1		c.296+3264A>G		intron	N/A	ENSP00000586639.1

Frequencies

GnomAD3 genomes AF: 0.500 AC: 76027 AN: 151906 Hom.: 19093 Cov.: 32

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.513

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.511

Gnomad OTH AF: 0.502

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

GnomAD4 genome AF: 0.501 AC: 76092 AN: 152024 Hom.: 19118 Cov.: 32 AF XY: 0.502 AC XY: 37274 AN XY: 74322

African (AFR) AF: 0.499 AC: 20683 AN: 41432

American (AMR) AF: 0.513 AC: 7832 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.546 AC: 1893 AN: 3468

East Asian (EAS) AF: 0.333 AC: 1721 AN: 5174

South Asian (SAS) AF: 0.425 AC: 2048 AN: 4820

European-Finnish (FIN) AF: 0.523 AC: 5524 AN: 10566

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.511 AC: 34757 AN: 67974

Other (OTH) AF: 0.499 AC: 1054 AN: 2112

Alfa AF: 0.509 Hom.: 31244

Bravo AF: 0.499

Asia WGS AF: 0.391 AC: 1364 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.66
DANN	Benign	0.65
PhyloP100		-1.0
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: rs1689924; hg19: chr1-20934796;