chrX-24465434-T-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_005391.5(PDK3):c.-22T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0374 in 1,145,267 control chromosomes in the GnomAD database, including 3,866 homozygotes. There are 13,566 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_005391.5 5_prime_UTR
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: 0.128 AC: 14337AN: 112191Hom.: 1637 Cov.: 24 AF XY: 0.128 AC XY: 4438AN XY: 34549
GnomAD3 exomes AF: 0.0834 AC: 10571AN: 126752Hom.: 943 AF XY: 0.0734 AC XY: 2606AN XY: 35482
GnomAD4 exome AF: 0.0275 AC: 28442AN: 1033031Hom.: 2229 Cov.: 21 AF XY: 0.0289 AC XY: 9122AN XY: 315987
GnomAD4 genome AF: 0.128 AC: 14343AN: 112236Hom.: 1637 Cov.: 24 AF XY: 0.128 AC XY: 4444AN XY: 34604
ClinVar
Submissions by phenotype
not specified Benign:1
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. -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at