14-29577354-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_002742.3(PRKD1):c.2623G>A(p.Glu875Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000564 in 1,613,710 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002742.3 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 |
---|---|---|---|---|---|---|---|---|
PRKD1 | NM_002742.3 | c.2623G>A | p.Glu875Lys | missense_variant | 18/18 | ENST00000331968.11 | NP_002733.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PRKD1 | ENST00000331968.11 | c.2623G>A | p.Glu875Lys | missense_variant | 18/18 | 1 | NM_002742.3 | ENSP00000333568 | P3 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152092Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000171 AC: 43AN: 250866Hom.: 0 AF XY: 0.000162 AC XY: 22AN XY: 135552
GnomAD4 exome AF: 0.0000575 AC: 84AN: 1461500Hom.: 0 Cov.: 31 AF XY: 0.0000660 AC XY: 48AN XY: 727054
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152210Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74420
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 14, 2022 | The c.2623G>A (p.E875K) alteration is located in exon 18 (coding exon 18) of the PRKD1 gene. This alteration results from a G to A substitution at nucleotide position 2623, causing the glutamic acid (E) at amino acid position 875 to be replaced by a lysine (K). 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