rs758706279
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Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The ENST00000507735.6(PALLD):c.123G>A(p.Pro41=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000183 in 1,496,568 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00093 ( 1 hom., cov: 32)
Exomes 𝑓: 0.000099 ( 1 hom. )
Consequence
PALLD
ENST00000507735.6 synonymous
ENST00000507735.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.970
Genes affected
PALLD (HGNC:17068): (palladin, cytoskeletal associated protein) This gene encodes a cytoskeletal protein that is required for organizing the actin cytoskeleton. The protein is a component of actin-containing microfilaments, and it is involved in the control of cell shape, adhesion, and contraction. Polymorphisms in this gene are associated with a susceptibility to pancreatic cancer type 1, and also with a risk for myocardial infarction. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009]
CBR4 (HGNC:25891): (carbonyl reductase 4) Enables several functions, including 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity; NADPH binding activity; and NADPH dehydrogenase (quinone) activity. Involved in fatty acid biosynthetic process; glycoside metabolic process; and protein tetramerization. Located in mitochondrial matrix. Part of oxidoreductase complex. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -17 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
?
Variant 4-168878014-G-A is Benign according to our data. Variant chr4-168878014-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 215801.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-0.97 with no splicing effect.
BS2
?
High AC in GnomAd4 at 141 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PALLD | NM_001166108.2 | c.1965-12908G>A | intron_variant | ENST00000505667.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PALLD | ENST00000505667.6 | c.1965-12908G>A | intron_variant | 1 | NM_001166108.2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.000922 AC: 140AN: 151840Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.0000749 AC: 7AN: 93402Hom.: 0 AF XY: 0.0000380 AC XY: 2AN XY: 52686
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GnomAD4 exome AF: 0.0000989 AC: 133AN: 1344620Hom.: 1 Cov.: 31 AF XY: 0.0000980 AC XY: 65AN XY: 663300
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GnomAD4 genome ? AF: 0.000928 AC: 141AN: 151948Hom.: 1 Cov.: 32 AF XY: 0.000781 AC XY: 58AN XY: 74286
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Pancreatic adenocarcinoma Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 23, 2023 | - - |
PALLD-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 10, 2019 | This variant is classified as 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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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at