rs61747430
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The ENST00000447079.6(CDK12):āc.3391A>Gā(p.Ile1131Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00162 in 1,614,184 control chromosomes in the GnomAD database, including 37 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
ENST00000447079.6 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/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CDK12 | NM_016507.4 | c.3391A>G | p.Ile1131Val | missense_variant | 13/14 | ENST00000447079.6 | NP_057591.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CDK12 | ENST00000447079.6 | c.3391A>G | p.Ile1131Val | missense_variant | 13/14 | 1 | NM_016507.4 | ENSP00000398880 | P4 | |
CDK12 | ENST00000430627.6 | c.3391A>G | p.Ile1131Val | missense_variant | 13/14 | 1 | ENSP00000407720 | A1 | ||
CDK12 | ENST00000584632.5 | c.3388A>G | p.Ile1130Val | missense_variant | 13/13 | 5 | ENSP00000464641 | |||
CDK12 | ENST00000559663.2 | c.3391A>G | p.Ile1131Val | missense_variant, NMD_transcript_variant | 13/21 | 5 | ENSP00000453329 |
Frequencies
GnomAD3 genomes AF: 0.00883 AC: 1344AN: 152178Hom.: 19 Cov.: 32
GnomAD3 exomes AF: 0.00241 AC: 605AN: 251406Hom.: 10 AF XY: 0.00167 AC XY: 227AN XY: 135870
GnomAD4 exome AF: 0.000866 AC: 1266AN: 1461888Hom.: 18 Cov.: 32 AF XY: 0.000708 AC XY: 515AN XY: 727244
GnomAD4 genome AF: 0.00882 AC: 1344AN: 152296Hom.: 19 Cov.: 32 AF XY: 0.00843 AC XY: 628AN XY: 74472
ClinVar
Submissions by phenotype
CDK12-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 21, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Hereditary breast ovarian cancer syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | National Health Laboratory Service, Universitas Academic Hospital and University of the Free State | Apr 19, 2022 | - - |
not specified Other:1
not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at