19-46674576-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_016457.5(PRKD2):c.2584C>T(p.Pro862Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000622 in 1,608,834 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_016457.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PRKD2 | NM_016457.5 | c.2584C>T | p.Pro862Ser | missense_variant | 18/18 | ENST00000291281.9 | NP_057541.2 | |
DACT3-AS1 | NR_040042.1 | n.189-2564G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PRKD2 | ENST00000291281.9 | c.2584C>T | p.Pro862Ser | missense_variant | 18/18 | 1 | NM_016457.5 | ENSP00000291281 | P1 | |
DACT3-AS1 | ENST00000690000.1 | n.1020-2564G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.00000671 AC: 1AN: 148980Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 249426Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135052
GnomAD4 exome AF: 0.00000617 AC: 9AN: 1459854Hom.: 0 Cov.: 31 AF XY: 0.00000964 AC XY: 7AN XY: 726276
GnomAD4 genome AF: 0.00000671 AC: 1AN: 148980Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 72740
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 09, 2023 | The c.2584C>T (p.P862S) alteration is located in exon 18 (coding exon 18) of the PRKD2 gene. This alteration results from a C to T substitution at nucleotide position 2584, causing the proline (P) at amino acid position 862 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at