rs186115112
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_006904.7(PRKDC):c.967-10G>T variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000635 in 1,562,170 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0034 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00034 ( 4 hom. )
Consequence
PRKDC
NM_006904.7 splice_polypyrimidine_tract, intron
NM_006904.7 splice_polypyrimidine_tract, intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.394
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 Likely_benign. Variant got -6 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
?
Variant 8-47939707-C-A is Benign according to our data. Variant chr8-47939707-C-A is described in ClinVar as [Benign]. Clinvar id is 542019.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRKDC | NM_006904.7 | c.967-10G>T | splice_polypyrimidine_tract_variant, intron_variant | ENST00000314191.7 | |||
PRKDC | NM_001081640.2 | c.967-10G>T | splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRKDC | ENST00000314191.7 | c.967-10G>T | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_006904.7 | P1 | |||
PRKDC | ENST00000338368.7 | c.967-10G>T | splice_polypyrimidine_tract_variant, intron_variant | 1 | |||||
PRKDC | ENST00000535375.1 | n.244G>T | non_coding_transcript_exon_variant | 1/2 | 3 | ||||
PRKDC | ENST00000697591.1 | n.1008-10G>T | splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.00339 AC: 515AN: 152116Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000748 AC: 157AN: 209944Hom.: 1 AF XY: 0.000575 AC XY: 66AN XY: 114764
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GnomAD4 exome AF: 0.000338 AC: 477AN: 1409936Hom.: 4 Cov.: 29 AF XY: 0.000284 AC XY: 199AN XY: 700412
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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 | Invitae | Jan 26, 2024 | - - |
Computational scores
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Name
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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