rs818199

Variant names:

• chr1-20597767-G-A
• rs818199
• NM_001785.3:c.155-7161G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-20597767-G-A
• chr1-20597767-G-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.155-7161G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.352 in 152,048 control chromosomes in the GnomAD database, including 9,773 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 0.35 (9773 hom., cov: 32)
• Consequence: CDA NM_001785.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.321
• Publications: 5 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDA	NM_001785.3	c.155-7161G>A		intron_variant	Intron 1 of 3	ENST00000375071.4	NP_001776.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDA	ENST00000375071.4	c.155-7161G>A		intron_variant	Intron 1 of 3	1	NM_001785.3	ENSP00000364212.3
CDA	ENST00000461985.1	n.199-7161G>A		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.352 AC: 53536 AN: 151930 Hom.: 9762 Cov.: 32

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.352 AC: 53561 AN: 152048 Hom.: 9773 Cov.: 32 AF XY: 0.353 AC XY: 26227 AN XY: 74322

African (AFR) AF: 0.248 AC: 10294 AN: 41486

American (AMR) AF: 0.425 AC: 6483 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.454 AC: 1576 AN: 3472

East Asian (EAS) AF: 0.448 AC: 2312 AN: 5162

South Asian (SAS) AF: 0.355 AC: 1711 AN: 4822

European-Finnish (FIN) AF: 0.310 AC: 3276 AN: 10562

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.392 AC: 26658 AN: 67970

Other (OTH) AF: 0.382 AC: 806 AN: 2108

Alfa AF: 0.379 Hom.: 28174

Bravo AF: 0.357

Asia WGS AF: 0.401 AC: 1396 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.46
PhyloP100		0.32
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: rs818199; hg19: chr1-20924260;