chr17-40289481-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001254.4(CDC6):c.61C>T(p.Arg21Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000105 in 1,613,816 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001254.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CDC6 | NM_001254.4 | c.61C>T | p.Arg21Trp | missense_variant | 2/12 | ENST00000209728.9 | NP_001245.1 | |
CDC6 | XM_011525541.3 | c.61C>T | p.Arg21Trp | missense_variant | 2/13 | XP_011523843.1 | ||
CDC6 | XM_011525542.2 | c.61C>T | p.Arg21Trp | missense_variant | 2/13 | XP_011523844.1 | ||
CDC6 | XM_047437207.1 | c.61C>T | p.Arg21Trp | missense_variant | 2/12 | XP_047293163.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CDC6 | ENST00000209728.9 | c.61C>T | p.Arg21Trp | missense_variant | 2/12 | 1 | NM_001254.4 | ENSP00000209728 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151988Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251488Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135916
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1461828Hom.: 0 Cov.: 32 AF XY: 0.0000110 AC XY: 8AN XY: 727214
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151988Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74206
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 30, 2021 | The c.61C>T (p.R21W) alteration is located in exon 2 (coding exon 1) of the CDC6 gene. This alteration results from a C to T substitution at nucleotide position 61, causing the arginine (R) at amino acid position 21 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at