rs8178225
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_006904.7(PRKDC):c.10211G>A(p.Gly3404Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0146 in 1,613,624 control chromosomes in the GnomAD database, including 230 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_006904.7 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRKDC | NM_006904.7 | c.10211G>A | p.Gly3404Glu | missense_variant | 72/86 | ENST00000314191.7 | |
PRKDC | NM_001081640.2 | c.10211G>A | p.Gly3404Glu | missense_variant | 72/85 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRKDC | ENST00000314191.7 | c.10211G>A | p.Gly3404Glu | missense_variant | 72/86 | 1 | NM_006904.7 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0120 AC: 1822AN: 152166Hom.: 20 Cov.: 32
GnomAD3 exomes AF: 0.0115 AC: 2866AN: 248590Hom.: 32 AF XY: 0.0111 AC XY: 1494AN XY: 134872
GnomAD4 exome AF: 0.0149 AC: 21794AN: 1461340Hom.: 210 Cov.: 30 AF XY: 0.0144 AC XY: 10492AN XY: 726952
GnomAD4 genome ? AF: 0.0120 AC: 1821AN: 152284Hom.: 20 Cov.: 32 AF XY: 0.0123 AC XY: 916AN XY: 74476
ClinVar
Submissions by phenotype
Severe combined immunodeficiency due to DNA-PKcs deficiency Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Feb 05, 2021 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 12, 2018 | 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