rs8178106
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_006904.7(PRKDC):c.4809G>T(p.Gln1603His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000842 in 1,613,976 control chromosomes in the GnomAD database, including 22 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 Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Q1603R) has been classified as Uncertain significance.
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.4809G>T | p.Gln1603His | missense_variant | 37/86 | ENST00000314191.7 | |
PRKDC | NM_001081640.2 | c.4809G>T | p.Gln1603His | missense_variant | 37/85 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRKDC | ENST00000314191.7 | c.4809G>T | p.Gln1603His | missense_variant | 37/86 | 1 | NM_006904.7 | P1 | |
PRKDC | ENST00000338368.7 | c.4809G>T | p.Gln1603His | missense_variant | 37/85 | 1 | |||
PRKDC | ENST00000697611.1 | n.913G>T | non_coding_transcript_exon_variant | 1/2 |
Frequencies
GnomAD3 genomes ? AF: 0.00114 AC: 173AN: 152218Hom.: 2 Cov.: 33
GnomAD3 exomes AF: 0.00405 AC: 1010AN: 249210Hom.: 17 AF XY: 0.00299 AC XY: 404AN XY: 135204
GnomAD4 exome AF: 0.000811 AC: 1186AN: 1461640Hom.: 20 Cov.: 31 AF XY: 0.000685 AC XY: 498AN XY: 727096
GnomAD4 genome ? AF: 0.00114 AC: 173AN: 152336Hom.: 2 Cov.: 33 AF XY: 0.00119 AC XY: 89AN XY: 74494
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 10, 2017 | 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. - |
Severe combined immunodeficiency due to DNA-PKcs deficiency Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 26, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at