1-20619151-C-T

Variant names:

• chr1-20619151-C-T
• rs10916832
• NM_001785.3:c.*583C>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.*583C>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.86 in 152,154 control chromosomes in the GnomAD database, including 56,772 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 0.86 (56772 hom., cov: 32)
• Consequence: CDA NM_001785.3 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.635
• Publications: 6 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=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.916 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDA	NM_001785.3	c.*583C>T		downstream_gene_variant		ENST00000375071.4	NP_001776.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDA	ENST00000375071.4	c.*583C>T		downstream_gene_variant		1	NM_001785.3	ENSP00000364212.3
CDA	ENST00000461985.1	n.*248C>T		downstream_gene_variant		3

Frequencies

GnomAD3 genomes AF: 0.860 AC: 130764 AN: 152036 Hom.: 56745 Cov.: 32

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.962

Gnomad AMR AF: 0.890

Gnomad ASJ AF: 0.934

Gnomad EAS AF: 0.685

Gnomad SAS AF: 0.723

Gnomad FIN AF: 0.889

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.922

Gnomad OTH AF: 0.886

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

GnomAD4 genome AF: 0.860 AC: 130841 AN: 152154 Hom.: 56772 Cov.: 32 AF XY: 0.856 AC XY: 63698 AN XY: 74378

African (AFR) AF: 0.767 AC: 31842 AN: 41514

American (AMR) AF: 0.890 AC: 13601 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.934 AC: 3242 AN: 3472

East Asian (EAS) AF: 0.686 AC: 3521 AN: 5136

South Asian (SAS) AF: 0.724 AC: 3490 AN: 4820

European-Finnish (FIN) AF: 0.889 AC: 9421 AN: 10602

Middle Eastern (MID) AF: 0.946 AC: 278 AN: 294

European-Non Finnish (NFE) AF: 0.922 AC: 62714 AN: 68010

Other (OTH) AF: 0.879 AC: 1855 AN: 2110

Alfa AF: 0.898 Hom.: 180936

Bravo AF: 0.858

Asia WGS AF: 0.709 AC: 2468 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.93
DANN	Benign	0.75
PhyloP100		-0.64

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10916832; hg19: chr1-20945644;