rs477155

chr1-20609755-G-Achr1-20609755-G-C

Variant summary

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

The NM_001785.3(CDA):c.267-4087G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.786 in 152,138 control chromosomes in the GnomAD database, including 47,415 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 0.79 (47415 hom., cov: 31)
• Consequence: CDA NM_001785.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.276

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=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.811 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDA	NM_001785.3	c.267-4087G>A		intron_variant		ENST00000375071.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDA	ENST00000375071.4	c.267-4087G>A		intron_variant		1	NM_001785.3	P1
CDA	ENST00000461985.1	n.310+4716G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.786 AC: 119529 AN: 152020 Hom.: 47393 Cov.: 31

Gnomad AFR AF: 0.778

Gnomad AMI AF: 0.812

Gnomad AMR AF: 0.763

Gnomad ASJ AF: 0.841

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.620

Gnomad FIN AF: 0.846

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.816

Gnomad OTH AF: 0.810

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

GnomAD4 genome AF: 0.786 AC: 119594 AN: 152138 Hom.: 47415 Cov.: 31 AF XY: 0.784 AC XY: 58299 AN XY: 74364

Gnomad4 AFR AF: 0.778

Gnomad4 AMR AF: 0.763

Gnomad4 ASJ AF: 0.841

Gnomad4 EAS AF: 0.500

Gnomad4 SAS AF: 0.620

Gnomad4 FIN AF: 0.846

Gnomad4 NFE AF: 0.816

Gnomad4 OTH AF: 0.804

Alfa AF: 0.814 Hom.: 45770

Bravo AF: 0.783

Asia WGS AF: 0.572 AC: 1994 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	3.3
Dann	Benign	0.75

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: rs477155; hg19: chr1-20936248;