11-65079496-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_080668.4(CDCA5):c.535G>A(p.Gly179Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00146 in 1,614,132 control chromosomes in the GnomAD database, including 37 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_080668.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CDCA5 | NM_080668.4 | c.535G>A | p.Gly179Arg | missense_variant | Exon 5 of 6 | ENST00000275517.8 | NP_542399.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00759 AC: 1155AN: 152120Hom.: 18 Cov.: 32
GnomAD3 exomes AF: 0.00206 AC: 518AN: 251432Hom.: 6 AF XY: 0.00154 AC XY: 209AN XY: 135908
GnomAD4 exome AF: 0.000822 AC: 1202AN: 1461894Hom.: 19 Cov.: 32 AF XY: 0.000716 AC XY: 521AN XY: 727248
GnomAD4 genome AF: 0.00759 AC: 1156AN: 152238Hom.: 18 Cov.: 32 AF XY: 0.00735 AC XY: 547AN XY: 74436
ClinVar
Submissions by phenotype
not provided Benign:2
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at