9-120389401-A-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_018249.6(CDK5RAP2):c.5626-109T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.736 in 866,718 control chromosomes in the GnomAD database, including 236,258 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_018249.6 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.768 AC: 116737AN: 152100Hom.: 45182 Cov.: 33
GnomAD4 exome AF: 0.729 AC: 520877AN: 714500Hom.: 191015 AF XY: 0.725 AC XY: 273336AN XY: 376966
GnomAD4 genome AF: 0.768 AC: 116857AN: 152218Hom.: 45243 Cov.: 33 AF XY: 0.771 AC XY: 57341AN XY: 74406
ClinVar
Submissions by phenotype
not provided Benign:2
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This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at