chr16-23626435-G-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_024675.4(PALB2):c.2587-38C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00122 in 1,612,100 control chromosomes in the GnomAD database, including 10 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0010 ( 1 hom., cov: 32)
Exomes 𝑓: 0.0012 ( 9 hom. )
Consequence
PALB2
NM_024675.4 intron
NM_024675.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.00400
Genes affected
PALB2 (HGNC:26144): (partner and localizer of BRCA2) This gene encodes a protein that may function in tumor suppression. This protein binds to and colocalizes with the breast cancer 2 early onset protein (BRCA2) in nuclear foci and likely permits the stable intranuclear localization and accumulation of BRCA2. [provided by RefSeq, Jul 2008]
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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=-0.84).
BP6
?
Variant 16-23626435-G-C is Benign according to our data. Variant chr16-23626435-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 126666.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-23626435-G-C is described in Lovd as [Likely_benign]. Variant chr16-23626435-G-C is described in Lovd as [Benign].
BS2
?
High Homozygotes in GnomAdExome at 2 AD,AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PALB2 | NM_024675.4 | c.2587-38C>G | intron_variant | ENST00000261584.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PALB2 | ENST00000261584.9 | c.2587-38C>G | intron_variant | 1 | NM_024675.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00104 AC: 158AN: 152128Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.00158 AC: 397AN: 251374Hom.: 2 AF XY: 0.00193 AC XY: 262AN XY: 135876
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GnomAD4 exome AF: 0.00124 AC: 1808AN: 1459854Hom.: 9 Cov.: 30 AF XY: 0.00140 AC XY: 1019AN XY: 726388
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GnomAD4 genome ? AF: 0.00103 AC: 157AN: 152246Hom.: 1 Cov.: 32 AF XY: 0.00116 AC XY: 86AN XY: 74442
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ClinVar
Significance: Likely benign
Submissions summary: Benign:4
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:2
Likely benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics Laboratory, Department of Pathology, Netherlands Cancer Institute | - | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital | Aug 15, 2023 | - - |
Familial cancer of breast Benign:1
Likely benign, no assertion criteria provided | curation | Leiden Open Variation Database | May 13, 2019 | Curators: Marc Tischkowitz, Arleen D. Auerbach. Submitter to LOVD: Marc Tischkowitz. - |
Computational scores
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BayesDel_noAF
Benign
Cadd
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Dann
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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