chr16-23622785-CT-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_024675.4(PALB2):c.2996+183del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00713 in 152,236 control chromosomes in the GnomAD database, including 15 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0071 ( 15 hom., cov: 32)
Consequence
PALB2
NM_024675.4 intron
NM_024675.4 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.528
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 Likely_benign. Variant got -6 ACMG points.
BP6
?
Variant 16-23622785-CT-C is Benign according to our data. Variant chr16-23622785-CT-C is described in ClinVar as [Benign]. Clinvar id is 126702.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-23622785-CT-C is described in Lovd as [Benign].
BS2
?
High Homozygotes in GnomAd at 15 AD,AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PALB2 | NM_024675.4 | c.2996+183del | intron_variant | ENST00000261584.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PALB2 | ENST00000261584.9 | c.2996+183del | intron_variant | 1 | NM_024675.4 | P1 | |||
ENST00000561764.1 | n.420-1114del | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00713 AC: 1085AN: 152118Hom.: 15 Cov.: 32
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GnomAD4 genome ? AF: 0.00713 AC: 1085AN: 152236Hom.: 15 Cov.: 32 AF XY: 0.00884 AC XY: 658AN XY: 74426
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 23, 2018 | - - |
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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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at