NM_024675.4:c.1830A>G

Variant names:

• chr16-23630324-T-C
• rs876659484
• NM_024675.4:c.1830A>G

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP6_Very_Strong BP7

The NM_024675.4(PALB2):​c.1830A>G​(p.Thr610Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000041 in 1,461,886 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000041 (0 hom.)
• Consequence: PALB2 NM_024675.4 synonymous
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:5
• Conservation: PhyloP100: 0.530
• Publications: 0 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: Benign. The variant received -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BP6: Variant 16-23630324-T-C is Benign according to our data. Variant chr16-23630324-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 231998.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-23630324-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 231998.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-23630324-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 231998.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-23630324-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 231998.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-23630324-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 231998.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-23630324-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 231998.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-23630324-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 231998.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-23630324-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 231998.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-23630324-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 231998.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-23630324-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 231998.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-23630324-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 231998.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-23630324-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 231998.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-23630324-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 231998.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-23630324-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 231998.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-23630324-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 231998.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-23630324-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 231998.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-23630324-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 231998.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-23630324-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 231998.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-23630324-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 231998.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-23630324-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 231998.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-23630324-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 231998.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-23630324-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 231998.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-23630324-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 231998.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-23630324-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 231998.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-23630324-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 231998.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-23630324-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 231998.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-23630324-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 231998.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-23630324-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 231998.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-23630324-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 231998.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-23630324-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 231998.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-23630324-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 231998.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-23630324-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 231998.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-23630324-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 231998.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=0.53 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PALB2	NM_024675.4	c.1830A>G	p.Thr610Thr	synonymous_variant	Exon 5 of 13	ENST00000261584.9	NP_078951.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PALB2	ENST00000261584.9	c.1830A>G	p.Thr610Thr	synonymous_variant	Exon 5 of 13	1	NM_024675.4	ENSP00000261584.4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000410 AC: 6 AN: 1461886 Hom.: 0 Cov.: 33 AF XY: 0.00000413 AC XY: 3 AN XY: 727242

African (AFR) AF: 0.00 AC: 0 AN: 33478

American (AMR) AF: 0.00 AC: 0 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26136

East Asian (EAS) AF: 0.00 AC: 0 AN: 39698

South Asian (SAS) AF: 0.00 AC: 0 AN: 86258

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53418

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5768

European-Non Finnish (NFE) AF: 0.00000540 AC: 6 AN: 1112010

Other (OTH) AF: 0.00 AC: 0 AN: 60396

GnomAD4 genome Cov.: 32

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Hereditary cancer-predisposing syndrome Benign:2

Mar 19, 2019

Color Diagnostics, LLC DBA Color Health

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jun 05, 2015

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. -

Familial cancer of breast Benign:2

Jan 14, 2025

Myriad Genetics, Inc.

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered benign. This variant is a silent/synonymous amino acid change and it is not expected to impact splicing. -

Sep 17, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not specified Benign:1

Jan 31, 2020

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

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	7.7
DANN	Benign	0.53
PhyloP100		0.53
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs876659484; hg19: chr16-23641645;