rs10916827

chr1-20606848-G-Achr1-20606848-G-T

Variant summary

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

The NM_001785.3(CDA):c.266+1809G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 152,044 control chromosomes in the GnomAD database, including 10,456 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 0.36 (10456 hom., cov: 32)
• Consequence: CDA NM_001785.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.325

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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDA	NM_001785.3	c.266+1809G>A		intron_variant		ENST00000375071.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDA	ENST00000375071.4	c.266+1809G>A		intron_variant		1	NM_001785.3	P1
CDA	ENST00000461985.1	n.310+1809G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.364 AC: 55353 AN: 151928 Hom.: 10451 Cov.: 32

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.364 AC: 55377 AN: 152044 Hom.: 10456 Cov.: 32 AF XY: 0.368 AC XY: 27335 AN XY: 74310

Gnomad4 AFR AF: 0.293

Gnomad4 AMR AF: 0.313

Gnomad4 ASJ AF: 0.392

Gnomad4 EAS AF: 0.358

Gnomad4 SAS AF: 0.471

Gnomad4 FIN AF: 0.498

Gnomad4 NFE AF: 0.391

Gnomad4 OTH AF: 0.354

Alfa AF: 0.376 Hom.: 10958

Bravo AF: 0.348

Asia WGS AF: 0.377 AC: 1312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.87
Dann	Benign	0.77

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: rs10916827; hg19: chr1-20933341;