1-1704076-T-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_024011.4(CDK11A):c.1757A>T(p.Gln586Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00239 in 1,595,632 control chromosomes in the GnomAD database, including 168 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 (★).
Frequency
Consequence
NM_024011.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDK11A | NM_024011.4 | c.1757A>T | p.Gln586Leu | missense_variant | 16/20 | ENST00000404249.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDK11A | ENST00000404249.8 | c.1757A>T | p.Gln586Leu | missense_variant | 16/20 | 1 | NM_024011.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00206 AC: 310AN: 150588Hom.: 11 Cov.: 31
GnomAD3 exomes AF: 0.00238 AC: 569AN: 238886Hom.: 11 AF XY: 0.00247 AC XY: 319AN XY: 129304
GnomAD4 exome AF: 0.00243 AC: 3508AN: 1444932Hom.: 157 Cov.: 37 AF XY: 0.00239 AC XY: 1714AN XY: 717236
GnomAD4 genome AF: 0.00206 AC: 310AN: 150700Hom.: 11 Cov.: 31 AF XY: 0.00232 AC XY: 171AN XY: 73606
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2023 | CDK11A: BP4, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at