rs201592874
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_006904.7(PRKDC):c.9933C>T(p.Asn3311=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000211 in 1,613,606 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00072 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00016 ( 1 hom. )
Consequence
PRKDC
NM_006904.7 synonymous
NM_006904.7 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0630
Genes affected
PRKDC (HGNC:9413): (protein kinase, DNA-activated, catalytic subunit) This gene encodes the catalytic subunit of the DNA-dependent protein kinase (DNA-PK). It functions with the Ku70/Ku80 heterodimer protein in DNA double strand break repair and recombination. The protein encoded is a member of the PI3/PI4-kinase family.[provided by RefSeq, Jul 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.76).
BP6
?
Variant 8-47800976-G-A is Benign according to our data. Variant chr8-47800976-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 508401.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=0.063 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRKDC | NM_006904.7 | c.9933C>T | p.Asn3311= | synonymous_variant | 71/86 | ENST00000314191.7 | |
PRKDC | NM_001081640.2 | c.9933C>T | p.Asn3311= | synonymous_variant | 71/85 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRKDC | ENST00000314191.7 | c.9933C>T | p.Asn3311= | synonymous_variant | 71/86 | 1 | NM_006904.7 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000723 AC: 110AN: 152118Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000551 AC: 137AN: 248642Hom.: 1 AF XY: 0.000393 AC XY: 53AN XY: 134866
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GnomAD4 exome AF: 0.000158 AC: 231AN: 1461370Hom.: 1 Cov.: 30 AF XY: 0.000128 AC XY: 93AN XY: 726942
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GnomAD4 genome ? AF: 0.000723 AC: 110AN: 152236Hom.: 0 Cov.: 32 AF XY: 0.000766 AC XY: 57AN XY: 74412
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 23, 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. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2024 | PRKDC: BP4, BP7 - |
Severe combined immunodeficiency due to DNA-PKcs deficiency Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 11, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at