NM_024675.4:c.2653C>T

Variant names:

• chr16-23626331-G-A
• rs878855111
• NM_024675.4:c.2653C>T

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 2P and 3B. PM2 BP4_Moderate BP6

The NM_024675.4(PALB2):​c.2653C>T​(p.Pro885Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P885T) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: PALB2 NM_024675.4 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1 B:1
• Conservation: PhyloP100: 0.958
• Publications: 1 publications found

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]

PALB2 Gene-Disease associations (from GenCC):

• hereditary breast carcinoma

  Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen, Ambry Genetics
• Fanconi anemia complementation group N

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae), ClinGen, Ambry Genetics
• pancreatic cancer, susceptibility to, 3

  Inheritance: AD Classification: STRONG Submitted by: Genomics England PanelApp, Labcorp Genetics (formerly Invitae)
• familial ovarian cancer

  Inheritance: AD Classification: MODERATE Submitted by: ClinGen
• Fanconi anemia

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• hereditary nonpolyposis colon cancer

  Inheritance: AD Classification: LIMITED Submitted by: ClinGen

ACMG classification

Our verdict: Likely_benign. The variant received -1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.18121532).
• BP6: Variant 16-23626331-G-A is Benign according to our data. Variant chr16-23626331-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 3228014. Variant chr16-23626331-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 3228014. Variant chr16-23626331-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 3228014. Variant chr16-23626331-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 3228014. Variant chr16-23626331-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 3228014. Variant chr16-23626331-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 3228014. Variant chr16-23626331-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 3228014. Variant chr16-23626331-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 3228014. Variant chr16-23626331-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 3228014. Variant chr16-23626331-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 3228014. Variant chr16-23626331-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 3228014. Variant chr16-23626331-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 3228014. Variant chr16-23626331-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 3228014. Variant chr16-23626331-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 3228014. Variant chr16-23626331-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 3228014. Variant chr16-23626331-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 3228014. Variant chr16-23626331-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 3228014. Variant chr16-23626331-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 3228014. Variant chr16-23626331-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 3228014. Variant chr16-23626331-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 3228014. Variant chr16-23626331-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 3228014. Variant chr16-23626331-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 3228014. Variant chr16-23626331-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 3228014. Variant chr16-23626331-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 3228014. Variant chr16-23626331-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 3228014. Variant chr16-23626331-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 3228014. Variant chr16-23626331-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 3228014. Variant chr16-23626331-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 3228014. Variant chr16-23626331-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 3228014. Variant chr16-23626331-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 3228014. Variant chr16-23626331-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 3228014. Variant chr16-23626331-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 3228014. Variant chr16-23626331-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 3228014.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PALB2	NM_024675.4	c.2653C>T	p.Pro885Ser	missense_variant	Exon 7 of 13	ENST00000261584.9	NP_078951.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PALB2	ENST00000261584.9	c.2653C>T	p.Pro885Ser	missense_variant	Exon 7 of 13	1	NM_024675.4	ENSP00000261584.4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:1 Benign:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Inherited breast cancer and ovarian cancer Uncertain:1

Apr 17, 2024

Genomics and Molecular Medicine Service, East Genomic Laboratory Hub, NHS Genomic Medicine Service

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

PM2_Supporting,BP1 -

Hereditary cancer-predisposing syndrome Benign:1

Feb 14, 2024

Ambry Genetics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.17
BayesDel_addAF	Benign	-0.20	T
BayesDel_noAF	Benign	-0.53
CADD	Benign	17
DANN	Uncertain	1.0
DEOGEN2	Benign	0.012	T;T
Eigen	Benign	-0.47
Eigen_PC	Benign	-0.47
FATHMM_MKL	Benign	0.16	N
LIST_S2	Benign	0.77	T;T
M_CAP	Benign	0.0076	T
MetaRNN	Benign	0.18	T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	1.9	.;L
PhyloP100		0.96
PrimateAI	Benign	0.34	T
PROVEAN	Uncertain	-3.5	D;D
REVEL	Benign	0.050
Sift	Benign	0.41	T;T
Sift4G	Benign	0.94	T;T
Polyphen		0.35	.;B
Vest4		0.28
MutPred		0.42		.;Loss of catalytic residue at P885 (P = 0.0123);
MVP		0.49
MPC		0.071
ClinPred		0.16	T
GERP RS		1.4
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.13
gMVP		0.43

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs878855111; hg19: chr16-23637652;