NM_001785.3:c.266+2751G>A

Variant names:

• chr1-20607790-G-A
• rs527912
• NM_001785.3:c.266+2751G>A

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+2751G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 152,098 control chromosomes in the GnomAD database, including 8,699 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 0.33 (8699 hom., cov: 32)
• Consequence: CDA NM_001785.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.644
• 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=-0.53).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.391 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+2751G>A		intron	N/A	NP_001776.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDA	ENST00000375071.4	TSL:1 MANE Select	c.266+2751G>A		intron	N/A	ENSP00000364212.3
	CDA	ENST00000904801.1		c.266+2751G>A		intron	N/A	ENSP00000574860.1
	CDA	ENST00000916580.1		c.296+2751G>A		intron	N/A	ENSP00000586639.1

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50888 AN: 151980 Hom.: 8697 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.335 AC: 50903 AN: 152098 Hom.: 8699 Cov.: 32 AF XY: 0.334 AC XY: 24792 AN XY: 74334

African (AFR) AF: 0.266 AC: 11043 AN: 41494

American (AMR) AF: 0.399 AC: 6097 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.432 AC: 1498 AN: 3468

East Asian (EAS) AF: 0.277 AC: 1433 AN: 5170

South Asian (SAS) AF: 0.295 AC: 1419 AN: 4818

European-Finnish (FIN) AF: 0.295 AC: 3122 AN: 10572

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.369 AC: 25099 AN: 67986

Other (OTH) AF: 0.358 AC: 757 AN: 2114

Alfa AF: 0.362 Hom.: 30256

Bravo AF: 0.340

Asia WGS AF: 0.296 AC: 1033 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	14
DANN	Benign	0.83
PhyloP100		0.64
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: rs527912; hg19: chr1-20934283;