chr16-2597749-G-A
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6BP7BS2
The NM_002613.5(PDPK1):c.1653G>A(p.Pro551=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000161 in 1,611,788 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000016 ( 1 hom. )
Consequence
PDPK1
NM_002613.5 synonymous
NM_002613.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.54
Genes affected
PDPK1 (HGNC:8816): (3-phosphoinositide dependent protein kinase 1) Enables 3-phosphoinositide-dependent protein kinase activity; phospholipase activator activity; and phospholipase binding activity. Involved in several processes, including cell surface receptor signaling pathway; regulation of protein kinase activity; and regulation of signal transduction. Acts upstream of or within intracellular signal transduction. Located in cell projection; cytosol; and plasma membrane. Implicated in prostate cancer. Biomarker of lung non-small cell carcinoma. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
Variant 16-2597749-G-A is Benign according to our data. Variant chr16-2597749-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3046933.Status of the report is no_assertion_criteria_provided, 0 stars.
BP7
Synonymous conserved (PhyloP=-1.54 with no splicing effect.
BS2
High AC in GnomAdExome4 at 24 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDPK1 | NM_002613.5 | c.1653G>A | p.Pro551= | synonymous_variant | 14/14 | ENST00000342085.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDPK1 | ENST00000342085.9 | c.1653G>A | p.Pro551= | synonymous_variant | 14/14 | 1 | NM_002613.5 | P1 | |
PDPK1 | ENST00000268673.11 | c.1272G>A | p.Pro424= | synonymous_variant | 11/11 | 1 | |||
PDPK1 | ENST00000441549.7 | c.*77G>A | 3_prime_UTR_variant | 12/12 | 1 | ||||
PDPK1 | ENST00000389224.7 | c.1572G>A | p.Pro524= | synonymous_variant | 14/14 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152228Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.00000799 AC: 2AN: 250216Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135486
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GnomAD4 exome AF: 0.0000164 AC: 24AN: 1459560Hom.: 1 Cov.: 30 AF XY: 0.0000165 AC XY: 12AN XY: 726138
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GnomAD4 genome AF: 0.0000131 AC: 2AN: 152228Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74370
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
PDPK1-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 13, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at