chr1-20604956-G-A
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_001785.3(CDA):c.183G>A(p.Pro61=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00146 in 1,613,456 control chromosomes in the GnomAD database, including 22 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0075 ( 10 hom., cov: 32)
Exomes 𝑓: 0.00083 ( 12 hom. )
Consequence
CDA
NM_001785.3 synonymous
NM_001785.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.31
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
?
Variant 1-20604956-G-A is Benign according to our data. Variant chr1-20604956-G-A is described in ClinVar as [Benign]. Clinvar id is 784935.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-2.31 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00749 (1141/152294) while in subpopulation AFR AF= 0.026 (1080/41550). AF 95% confidence interval is 0.0247. There are 10 homozygotes in gnomad4. There are 526 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 9 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDA | NM_001785.3 | c.183G>A | p.Pro61= | synonymous_variant | 2/4 | ENST00000375071.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDA | ENST00000375071.4 | c.183G>A | p.Pro61= | synonymous_variant | 2/4 | 1 | NM_001785.3 | P1 | |
CDA | ENST00000461985.1 | n.227G>A | non_coding_transcript_exon_variant | 2/3 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00748 AC: 1138AN: 152176Hom.: 9 Cov.: 32
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GnomAD3 exomes AF: 0.00201 AC: 503AN: 250606Hom.: 5 AF XY: 0.00149 AC XY: 202AN XY: 135420
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GnomAD4 exome AF: 0.000834 AC: 1218AN: 1461162Hom.: 12 Cov.: 30 AF XY: 0.000704 AC XY: 512AN XY: 726884
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GnomAD4 genome ? AF: 0.00749 AC: 1141AN: 152294Hom.: 10 Cov.: 32 AF XY: 0.00706 AC XY: 526AN XY: 74478
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Mar 29, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at