16-23607859-C-T

Position:

• chr16-23607859-C-T

Variant summary

Our verdict is Likely pathogenic. Variant got 7 ACMG points: 8P and 1B. PP5_Very_Strong BP4

The NM_024675.4(PALB2):​c.3350+5G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000821 in 1,461,520 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★★).

• Frequency:
  • Genomes: 𝑓 0.0000066 (0 hom., cov: 31)
  • Exomes 𝑓: 0.0000082 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: PALB2 NM_024675.4 splice_region, intron
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:10
• Conservation: PhyloP100: 3.40

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]

ENSG00000261723 (HGNC:):

ACMG classification

Verdict is Likely_pathogenic. Variant got 7 ACMG points.

• PP5: Variant 16-23607859-C-T is Pathogenic according to our data. Variant chr16-23607859-C-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 142586.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.32). . Strength limited to SUPPORTING due to the PP5.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PALB2	NM_024675.4	c.3350+5G>A		splice_region_variant, intron_variant		ENST00000261584.9	NP_078951.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PALB2	ENST00000261584.9	c.3350+5G>A		splice_region_variant, intron_variant		1	NM_024675.4	ENSP00000261584.4

Frequencies

GnomAD3 genomes AF: 0.00 AC: 1 AN: 152170 Hom.: 0 Cov.: 31 FAILED QC

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.00000796 AC: 2 AN: 251408 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 135870

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.0000578

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000821 AC: 12 AN: 1461520 Hom.: 0 Cov.: 31 AF XY: 0.00000963 AC XY: 7 AN XY: 727058

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000447

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.000202

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 8.99e-7

Gnomad4 OTH exome AF: 0.0000166

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000657 AC: 1 AN: 152288 Hom.: 0 Cov.: 31 AF XY: 0.0000134 AC XY: 1 AN XY: 74460

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:10

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Hereditary cancer-predisposing syndrome Pathogenic:4

Likely pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Jan 25, 2024	The c.3350+5G>A intronic variant results from a G to A substitution 5 nucleotides after coding exon 12 in the PALB2 gene. This nucleotide position is highly conserved in available vertebrate species. This alteration has been identified in the homozygous state in an individual with Fanconi Anemia features and RNA analysis showed skipping of coding exon 12 (Mori M et al. Haematologica. 2019 Oct;104:1962-1973). In silico splice site analysis for this alteration is inconclusive. RNA studies have demonstrated this alteration results in abnormal splicing in the set of samples tested (Ambry internal data). Based on the majority of available evidence to date, this variant is likely to be pathogenic. -
Likely pathogenic, criteria provided, single submitter	curation	Sema4, Sema4	Jan 27, 2021	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Feb 21, 2023	This variant causes a G to A nucleotide substitution at the +5 position of the intron 12 splice donor site of the PALB2 gene. Four RNA studies have reported aberrant mRNA transcripts in variant carriers and in one minigene splicing assay that are predicted to disrupt the BRCA2 and RAD51 binding domain in the protein (PMID: 30792206, 30890586, 32133419, 32238468, 34846068). One of the aberrant transcript is also present in healthy controls, albeit at a lower average level than in carriers with this variant (PMID: 32133419). This variant has been reported in two individuals affected with breast cancer, one individual affected with pancreatic cancer who also has a ATM truncation variant, and another individual affected with ovarian cancer (PMID: 29731985, 34793666, 35676859). The variant also has been observed in a homozygous carrier affected with Fanconi anemia (PMID: 30792206, 32238468). This variant has been identified in 2/251408 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Loss of PALB2 function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Likely Pathogenic. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Mendelics	Mar 30, 2023	- -

Familial cancer of breast Pathogenic:3

Likely pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Aug 28, 2023	- -
Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 19, 2024	This sequence change falls in intron 12 of the PALB2 gene. It does not directly change the encoded amino acid sequence of the PALB2 protein. RNA analysis indicates that this variant induces altered splicing and likely disrupts the C-terminus of the protein. This variant is present in population databases (rs587782566, gnomAD 0.006%). This variant has been observed in individual(s) with Fanconi anemia (PMID: 30792206). ClinVar contains an entry for this variant (Variation ID: 142586). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant results in the generation of two aberrant transcripts, one that leads to out-of-frame exon 12 skipping and the other that leads to the in-frame skipping of exons 11 and 12 together and introduces a new termination codon (PMID: 30890586, 32133419; Invitae). However the mRNA is not expected to undergo nonsense-mediated decay. This variant disrupts a region of the PALB2 protein in which other variant(s) (p.Tyr1183*) have been determined to be pathogenic (PMID: 17200671, 20927582, 21165770, 21365267, 26283626, 26296701). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Myriad Genetics, Inc.	Oct 06, 2023	This variant is considered likely pathogenic. mRNA analysis has demonstrated abnormal mRNA splicing occurs [PMID: 30792206, 32133419, 34846068]. This variant has been observed homozygous in one or more individuals with Fanconi Anemia [PMID: 30792206]. -

PALB2-related disorder Pathogenic:1

Likely pathogenic, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Jun 22, 2024

The PALB2 c.3350+5G>A variant is predicted to interfere with splicing. This variant has been reported in the homozygous state in an individual with Fanconi anemia (Mori et al 2019. PubMed ID: 30792206). It has also been described in individuals with breast or pancreatic cancer, and two of these individuals also carried a frameshift variant in ATM (Kondo et al. 2018. PubMed ID: 29731985; Megid et al. 2022. PubMed ID: 36003761; Park et al. 2021. PubMed ID: 34793666). RNA studies indicate this variant causes exon 12 skipping (Mori et al. 2019. PubMed ID: 30792206; Lopez-Perolio et al. 2019. PubMed ID: 30890586; Valenzuela-Palomo et al. 2021. PubMed ID: 34846068). This variant is reported in 0.0058% of alleles in individuals of Latino descent in gnomAD and is interpreted as pathogenic or likely pathogenic in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/142586/). This variant is interpreted as likely pathogenic. -

Fanconi anemia complementation group N;C3150547:Pancreatic cancer, susceptibility to, 3;C5830615:Breast-ovarian cancer, familial, susceptibility to, 5 Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Juno Genomics, Hangzhou Juno Genomics, Inc

-

PVS1+PM3_Supporting -

Hereditary breast ovarian cancer syndrome Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Jan 31, 2022

Variant summary: PALB2 c.3350+5G>A alters a conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. One computational tool predicts the variant weakens a 5' donor site. Experimental evidence from multiple studies demonstrate that this variant affects mRNA splicing leading to aberrant transcripts, most significantly to skipping of exon 12 (Karam_2019, Lopez-Perolio_2019, Mori_2019, Landrith_2020). Some of these studies identified naturally occurring alternative splicing event(s) leading to skipping of exon 12. However, the variant causes a significant increase to the level of alternative splicing resulting in skipping of this exon. The predicted protein encoded by this transcript is unlikely to be functional, as it lacks part of the C-terminal WD40 beta-propeller domain that mediates PALB2 interaction with several key homologous recombination proteins, including BRCA2 and RAD51 (Lopez-Perolio_2019, Landrith_2020). The variant allele was found at a frequency of 8e-06 in 251408 control chromosomes (gnomAD). c.3350+5G>A has been reported in the literature in individuals affected with Hereditary Breast And Ovarian Cancer Syndrome and pancreatic ductal adenocarcinoma (e.g. Kondo_2018, Landrith_2020). It was also reported in a homozygous individual affected with Fanconi Anemia (Mori_2019). Three ClinVar submitters (evaluation after 2014) cite the variant as likely pathogenic and one ClinVar submitter (evaluation after 2014) cites it as uncertain significance. Based on the evidence outlined above, the variant was classified as likely pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.32
CADD	Benign	19
DANN	Benign	0.93

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.14		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs587782566; hg19: chr16-23619180;