8-47826778-G-A
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_006904.7(PRKDC):c.8661C>T(p.Pro2887=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000973 in 1,611,454 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts 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. P2887P) has been classified as Likely benign.
Frequency
Consequence
NM_006904.7 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRKDC | NM_006904.7 | c.8661C>T | p.Pro2887= | synonymous_variant | 63/86 | ENST00000314191.7 | |
PRKDC | NM_001081640.2 | c.8661C>T | p.Pro2887= | synonymous_variant | 63/85 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRKDC | ENST00000314191.7 | c.8661C>T | p.Pro2887= | synonymous_variant | 63/86 | 1 | NM_006904.7 | P1 | |
PRKDC | ENST00000338368.7 | c.8661C>T | p.Pro2887= | synonymous_variant | 63/85 | 1 | |||
PRKDC | ENST00000697603.1 | c.1338C>T | p.Pro446= | synonymous_variant | 10/33 |
Frequencies
GnomAD3 genomes AF: 0.00484 AC: 736AN: 152220Hom.: 8 Cov.: 33
GnomAD3 exomes AF: 0.00133 AC: 322AN: 241704Hom.: 1 AF XY: 0.000940 AC XY: 124AN XY: 131872
GnomAD4 exome AF: 0.000572 AC: 834AN: 1459116Hom.: 4 Cov.: 31 AF XY: 0.000462 AC XY: 335AN XY: 725626
GnomAD4 genome AF: 0.00482 AC: 734AN: 152338Hom.: 8 Cov.: 33 AF XY: 0.00450 AC XY: 335AN XY: 74486
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 24, 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. - |
Severe combined immunodeficiency due to DNA-PKcs deficiency Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at