chr17-40289534-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001254.4(CDC6):c.114T>G(p.Asn38Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/23 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. N38N) has been classified as Likely benign.
Frequency
Consequence
NM_001254.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDC6 | NM_001254.4 | c.114T>G | p.Asn38Lys | missense_variant | 2/12 | ENST00000209728.9 | |
CDC6 | XM_011525541.3 | c.114T>G | p.Asn38Lys | missense_variant | 2/13 | ||
CDC6 | XM_011525542.2 | c.114T>G | p.Asn38Lys | missense_variant | 2/13 | ||
CDC6 | XM_047437207.1 | c.114T>G | p.Asn38Lys | missense_variant | 2/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDC6 | ENST00000209728.9 | c.114T>G | p.Asn38Lys | missense_variant | 2/12 | 1 | NM_001254.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD4 exome Cov.: 32
GnomAD4 genome ? Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 04, 2024 | The c.114T>G (p.N38K) alteration is located in exon 2 (coding exon 1) of the CDC6 gene. This alteration results from a T to G substitution at nucleotide position 114, causing the asparagine (N) at amino acid position 38 to be replaced by a lysine (K). 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
Publications
No publications associated with this variant yet.