8-47960111-C-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The ENST00000314191.7(PRKDC):c.16G>T(p.Ala6Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0058 in 1,504,624 control chromosomes in the GnomAD database, including 352 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/18 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. A6V) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000314191.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PRKDC | NM_006904.7 | c.16G>T | p.Ala6Ser | missense_variant | 1/86 | ENST00000314191.7 | NP_008835.5 | |
PRKDC | NM_001081640.2 | c.16G>T | p.Ala6Ser | missense_variant | 1/85 | NP_001075109.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PRKDC | ENST00000314191.7 | c.16G>T | p.Ala6Ser | missense_variant | 1/86 | 1 | NM_006904.7 | ENSP00000313420 | P1 | |
PRKDC | ENST00000338368.7 | c.16G>T | p.Ala6Ser | missense_variant | 1/85 | 1 | ENSP00000345182 | |||
PRKDC | ENST00000697591.1 | n.57G>T | non_coding_transcript_exon_variant | 1/15 |
Frequencies
GnomAD3 genomes AF: 0.0284 AC: 4328AN: 152168Hom.: 216 Cov.: 32
GnomAD3 exomes AF: 0.00550 AC: 585AN: 106398Hom.: 19 AF XY: 0.00463 AC XY: 274AN XY: 59214
GnomAD4 exome AF: 0.00324 AC: 4379AN: 1352344Hom.: 136 Cov.: 31 AF XY: 0.00299 AC XY: 1991AN XY: 664850
GnomAD4 genome AF: 0.0285 AC: 4341AN: 152280Hom.: 216 Cov.: 32 AF XY: 0.0274 AC XY: 2041AN XY: 74456
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2016 | 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
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Severe combined immunodeficiency due to DNA-PKcs deficiency Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at