rs200510022
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_006904.7(PRKDC):āc.6348T>Cā(p.Asp2116=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00109 in 1,511,178 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_006904.7 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRKDC | NM_006904.7 | c.6348T>C | p.Asp2116= | splice_region_variant, synonymous_variant | 48/86 | ENST00000314191.7 | |
PRKDC | NM_001081640.2 | c.6348T>C | p.Asp2116= | splice_region_variant, synonymous_variant | 48/85 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRKDC | ENST00000314191.7 | c.6348T>C | p.Asp2116= | splice_region_variant, synonymous_variant | 48/86 | 1 | NM_006904.7 | P1 | |
PRKDC | ENST00000338368.7 | c.6348T>C | p.Asp2116= | splice_region_variant, synonymous_variant | 48/85 | 1 | |||
PRKDC | ENST00000697609.1 | n.509T>C | splice_region_variant, non_coding_transcript_exon_variant | 2/4 | |||||
PRKDC | ENST00000697610.1 | n.149T>C | splice_region_variant, non_coding_transcript_exon_variant | 3/4 |
Frequencies
GnomAD3 genomes ? AF: 0.000696 AC: 106AN: 152234Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000738 AC: 102AN: 138126Hom.: 0 AF XY: 0.000895 AC XY: 66AN XY: 73782
GnomAD4 exome AF: 0.00113 AC: 1534AN: 1358826Hom.: 1 Cov.: 30 AF XY: 0.00116 AC XY: 775AN XY: 668222
GnomAD4 genome ? AF: 0.000696 AC: 106AN: 152352Hom.: 0 Cov.: 33 AF XY: 0.000671 AC XY: 50AN XY: 74508
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2022 | PRKDC: BP4, BP7 - |
Severe combined immunodeficiency due to DNA-PKcs deficiency Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at