chr10-60788210-A-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001786.5(CDK1):āc.469A>Gā(p.Ile157Val) variant causes a missense change. The variant allele was found at a frequency of 0.00000869 in 1,610,524 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I157L) has been classified as Uncertain significance.
Frequency
Consequence
NM_001786.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDK1 | NM_001786.5 | c.469A>G | p.Ile157Val | missense_variant | 5/8 | ENST00000395284.8 | |
CDK1 | NM_001320918.1 | c.469A>G | p.Ile157Val | missense_variant | 5/8 | ||
CDK1 | XM_005270303.4 | c.469A>G | p.Ile157Val | missense_variant | 5/8 | ||
CDK1 | NM_033379.5 | c.318+2423A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDK1 | ENST00000395284.8 | c.469A>G | p.Ile157Val | missense_variant | 5/8 | 1 | NM_001786.5 | P3 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152100Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000324 AC: 8AN: 247244Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 134214
GnomAD4 exome AF: 0.00000891 AC: 13AN: 1458424Hom.: 0 Cov.: 29 AF XY: 0.00000414 AC XY: 3AN XY: 725464
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152100Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74294
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 12, 2022 | The c.469A>G (p.I157V) alteration is located in exon 5 (coding exon 4) of the CDK1 gene. This alteration results from a A to G substitution at nucleotide position 469, causing the isoleucine (I) at amino acid position 157 to be replaced by a valine (V). 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