chr8-47820838-G-A
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_006904.7(PRKDC):c.9217C>T(p.Leu3073Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000543 in 1,613,354 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. L3073L) has been classified as Likely benign.
Frequency
Consequence
NM_006904.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRKDC | NM_006904.7 | c.9217C>T | p.Leu3073Phe | missense_variant | 66/86 | ENST00000314191.7 | |
PRKDC | NM_001081640.2 | c.9217C>T | p.Leu3073Phe | missense_variant | 66/85 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRKDC | ENST00000314191.7 | c.9217C>T | p.Leu3073Phe | missense_variant | 66/86 | 1 | NM_006904.7 | P1 | |
PRKDC | ENST00000338368.7 | c.9217C>T | p.Leu3073Phe | missense_variant | 66/85 | 1 | |||
PRKDC | ENST00000697603.1 | c.1894C>T | p.Leu632Phe | missense_variant | 13/33 |
Frequencies
GnomAD3 genomes AF: 0.00268 AC: 407AN: 152018Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.000738 AC: 184AN: 249276Hom.: 1 AF XY: 0.000436 AC XY: 59AN XY: 135242
GnomAD4 exome AF: 0.000320 AC: 468AN: 1461218Hom.: 2 Cov.: 30 AF XY: 0.000270 AC XY: 196AN XY: 726912
GnomAD4 genome AF: 0.00268 AC: 408AN: 152136Hom.: 2 Cov.: 32 AF XY: 0.00239 AC XY: 178AN XY: 74382
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 31, 2018 | - - |
Severe combined immunodeficiency due to DNA-PKcs deficiency Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 04, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at