rs8178111
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_006904.7(PRKDC):c.5235+10T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000563 in 1,557,436 control chromosomes in the GnomAD database, including 13 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00068 ( 3 hom., cov: 32)
Exomes 𝑓: 0.00055 ( 10 hom. )
Consequence
PRKDC
NM_006904.7 intron
NM_006904.7 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.00100
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 -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BP6
Variant 8-47879481-A-T is Benign according to our data. Variant chr8-47879481-A-T is described in ClinVar as [Benign]. Clinvar id is 475230.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.000683 (104/152356) while in subpopulation EAS AF= 0.0191 (99/5184). AF 95% confidence interval is 0.0161. There are 3 homozygotes in gnomad4. There are 59 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 3 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PRKDC | NM_006904.7 | c.5235+10T>A | intron_variant | ENST00000314191.7 | NP_008835.5 | |||
PRKDC | NM_001081640.2 | c.5235+10T>A | intron_variant | NP_001075109.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PRKDC | ENST00000314191.7 | c.5235+10T>A | intron_variant | 1 | NM_006904.7 | ENSP00000313420.3 | ||||
PRKDC | ENST00000338368.7 | c.5235+10T>A | intron_variant | 1 | ENSP00000345182.4 |
Frequencies
GnomAD3 genomes AF: 0.000683 AC: 104AN: 152238Hom.: 3 Cov.: 32
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GnomAD3 exomes AF: 0.00152 AC: 288AN: 189844Hom.: 4 AF XY: 0.00134 AC XY: 136AN XY: 101554
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GnomAD4 exome AF: 0.000550 AC: 773AN: 1405080Hom.: 10 Cov.: 31 AF XY: 0.000526 AC XY: 364AN XY: 692632
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GnomAD4 genome AF: 0.000683 AC: 104AN: 152356Hom.: 3 Cov.: 32 AF XY: 0.000792 AC XY: 59AN XY: 74518
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Severe combined immunodeficiency due to DNA-PKcs deficiency Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 04, 2024 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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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