rs772883495
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_006904.7(PRKDC):āc.1389G>Cā(p.Lys463Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000041 in 1,461,698 control chromosomes in the GnomAD database, with no homozygous occurrence. 12/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. K463E) has been classified as Uncertain significance.
Frequency
Consequence
NM_006904.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRKDC | NM_006904.7 | c.1389G>C | p.Lys463Asn | missense_variant | 13/86 | ENST00000314191.7 | |
PRKDC | NM_001081640.2 | c.1389G>C | p.Lys463Asn | missense_variant | 13/85 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRKDC | ENST00000314191.7 | c.1389G>C | p.Lys463Asn | missense_variant | 13/86 | 1 | NM_006904.7 | P1 | |
PRKDC | ENST00000338368.7 | c.1389G>C | p.Lys463Asn | missense_variant | 13/85 | 1 | |||
PRKDC | ENST00000697591.1 | n.1430G>C | non_coding_transcript_exon_variant | 13/15 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249284Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135236
GnomAD4 exome AF: 0.00000410 AC: 6AN: 1461698Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 727128
GnomAD4 genome ? Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at