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dbSNP Short Genetic Variations

Reference SNP (rs) Report

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This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs869312772

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr16:23635383-23635384 (GRCh38.p7) Help

The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.

Alleles
delG / dupG
Variation Type
Indel Insertion and Deletion
Frequency
None
Clinical Significance
Reported in ClinVar
Gene : Consequence
PALB2 : Frameshift
Publications
1 citation
Genomic View
See rs on genome
Help

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements
Sequence name Change
GRCh38.p7 chr 16 NC_000016.10:g.23635384delG
GRCh38.p7 chr 16 NC_000016.10:g.23635384dup
GRCh37.p13 chr 16 NC_000016.9:g.23646705delG
GRCh37.p13 chr 16 NC_000016.9:g.23646705dup
PALB2 RefSeqGene (LRG_308) NG_007406.1:g.10975delC
PALB2 RefSeqGene (LRG_308) NG_007406.1:g.10975dup
Gene: PALB2, partner and localizer of BRCA2 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
PALB2 transcript NM_024675.3:c.116...

NM_024675.3:c.1163delC

P [CCT] > L [CT] Coding Sequence Variant
partner and localizer of BRCA2 NP_078951.2:p.Pro...

NP_078951.2:p.Pro388fs

P (Pro) > L (Leu) Frameshift
PALB2 transcript NM_024675.3:c.116...

NM_024675.3:c.1163dup

P [CCT] > P [CCCT] Coding Sequence Variant
partner and localizer of BRCA2 NP_078951.2:p.Pro...

NP_078951.2:p.Pro388fs

P (Pro) > P (Pro) Frameshift
PALB2 transcript variant X1 XM_011545946.2:c....

XM_011545946.2:c.1169delC

P [CCT] > L [CT] Coding Sequence Variant
partner and localizer of BRCA2 isoform X1 XP_011544248.1:p....

XP_011544248.1:p.Pro390fs

P (Pro) > L (Leu) Frameshift
PALB2 transcript variant X1 XM_011545946.2:c....

XM_011545946.2:c.1169dup

P [CCT] > P [CCCT] Coding Sequence Variant
partner and localizer of BRCA2 isoform X1 XP_011544248.1:p....

XP_011544248.1:p.Pro390fs

P (Pro) > P (Pro) Frameshift
PALB2 transcript variant X2 XM_017023671.1:c....

XM_017023671.1:c.1169delC

P [CCT] > L [CT] Coding Sequence Variant
partner and localizer of BRCA2 isoform X2 XP_016879160.1:p....

XP_016879160.1:p.Pro390fs

P (Pro) > L (Leu) Frameshift
PALB2 transcript variant X2 XM_017023671.1:c....

XM_017023671.1:c.1169dup

P [CCT] > P [CCCT] Coding Sequence Variant
partner and localizer of BRCA2 isoform X2 XP_016879160.1:p....

XP_016879160.1:p.Pro390fs

P (Pro) > P (Pro) Frameshift
PALB2 transcript variant X3 XM_017023672.1:c....

XM_017023672.1:c.1163delC

P [CCT] > L [CT] Coding Sequence Variant
partner and localizer of BRCA2 isoform X3 XP_016879161.1:p....

XP_016879161.1:p.Pro388fs

P (Pro) > L (Leu) Frameshift
PALB2 transcript variant X3 XM_017023672.1:c....

XM_017023672.1:c.1163dup

P [CCT] > P [CCCT] Coding Sequence Variant
partner and localizer of BRCA2 isoform X3 XP_016879161.1:p....

XP_016879161.1:p.Pro388fs

P (Pro) > P (Pro) Frameshift
PALB2 transcript variant X4 XM_011545947.2:c....

XM_011545947.2:c.1169delC

P [CCT] > L [CT] Coding Sequence Variant
partner and localizer of BRCA2 isoform X4 XP_011544249.1:p....

XP_011544249.1:p.Pro390fs

P (Pro) > L (Leu) Frameshift
PALB2 transcript variant X4 XM_011545947.2:c....

XM_011545947.2:c.1169dup

P [CCT] > P [CCCT] Coding Sequence Variant
partner and localizer of BRCA2 isoform X4 XP_011544249.1:p....

XP_011544249.1:p.Pro390fs

P (Pro) > P (Pro) Frameshift
PALB2 transcript variant X5 XM_017023673.1:c....

XM_017023673.1:c.1163delC

P [CCT] > L [CT] Coding Sequence Variant
partner and localizer of BRCA2 isoform X5 XP_016879162.1:p....

XP_016879162.1:p.Pro388fs

P (Pro) > L (Leu) Frameshift
PALB2 transcript variant X5 XM_017023673.1:c....

XM_017023673.1:c.1163dup

P [CCT] > P [CCCT] Coding Sequence Variant
partner and localizer of BRCA2 isoform X5 XP_016879162.1:p....

XP_016879162.1:p.Pro388fs

P (Pro) > P (Pro) Frameshift
PALB2 transcript variant X6 XM_011545948.2:c....

XM_011545948.2:c.278delC

P [CCT] > L [CT] Coding Sequence Variant
partner and localizer of BRCA2 isoform X6 XP_011544250.1:p....

XP_011544250.1:p.Pro93fs

P (Pro) > L (Leu) Frameshift
PALB2 transcript variant X6 XM_011545948.2:c....

XM_011545948.2:c.278dup

P [CCT] > P [CCCT] Coding Sequence Variant
partner and localizer of BRCA2 isoform X6 XP_011544250.1:p....

XP_011544250.1:p.Pro93fs

P (Pro) > P (Pro) Frameshift
Help

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Allele: delG (allele ID: 226360 )
ClinVar Accession Disease Names Clinical Significance
RCV000210113.1 Hereditary cancer-predisposing syndrome Pathogenic
Allele: dupG (allele ID: 409560 )
ClinVar Accession Disease Names Clinical Significance
RCV000479016.1 not provided Likely-Pathogenic
RCV000568264.1 Hereditary cancer-predisposing syndrome Pathogenic
RCV000635719.1 Familial cancer of breast Pathogenic
Help

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

None
Help

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement GG= delG dupG Note
GRCh38.p7 chr 16 NC_000016.10:g.23...

NC_000016.10:g.23635383_23635384GG=

NC_000016.10:g.23...

NC_000016.10:g.23635384delG

NC_000016.10:g.23...

NC_000016.10:g.23635384dup

GRCh37.p13 chr 16 NC_000016.9:g.236...

NC_000016.9:g.23646704_23646705GG=

NC_000016.9:g.236...

NC_000016.9:g.23646705delG

NC_000016.9:g.236...

NC_000016.9:g.23646705dup

PALB2 RefSeqGene (LRG_308) NG_007406.1:g.109...

NG_007406.1:g.10974_10975CC=

NG_007406.1:g.109...

NG_007406.1:g.10975delC

NG_007406.1:g.109...

NG_007406.1:g.10975dup

PALB2 transcript NM_024675.3:c.116...

NM_024675.3:c.1162_1163CC=

NM_024675.3:c.116...

NM_024675.3:c.1163delC

NM_024675.3:c.116...

NM_024675.3:c.1163dup

PALB2 transcript variant X1 XM_011545946.2:c....

XM_011545946.2:c.1168_1169CC=

XM_011545946.2:c....

XM_011545946.2:c.1169delC

XM_011545946.2:c....

XM_011545946.2:c.1169dup

PALB2 transcript variant X4 XM_011545947.2:c....

XM_011545947.2:c.1168_1169CC=

XM_011545947.2:c....

XM_011545947.2:c.1169delC

XM_011545947.2:c....

XM_011545947.2:c.1169dup

PALB2 transcript variant X6 XM_011545948.2:c....

XM_011545948.2:c.277_278CC=

XM_011545948.2:c....

XM_011545948.2:c.278delC

XM_011545948.2:c....

XM_011545948.2:c.278dup

PALB2 transcript variant X2 XM_017023671.1:c....

XM_017023671.1:c.1168_1169CC=

XM_017023671.1:c....

XM_017023671.1:c.1169delC

XM_017023671.1:c....

XM_017023671.1:c.1169dup

PALB2 transcript variant X5 XM_017023673.1:c....

XM_017023673.1:c.1162_1163CC=

XM_017023673.1:c....

XM_017023673.1:c.1163delC

XM_017023673.1:c....

XM_017023673.1:c.1163dup

PALB2 transcript variant X3 XM_017023672.1:c....

XM_017023672.1:c.1162_1163CC=

XM_017023672.1:c....

XM_017023672.1:c.1163delC

XM_017023672.1:c....

XM_017023672.1:c.1163dup

partner and localizer of BRCA2 NP_078951.2:p.Pro...

NP_078951.2:p.Pro388=

NP_078951.2:p.Pro...

NP_078951.2:p.Pro388fs

NP_078951.2:p.Pro...

NP_078951.2:p.Pro388fs

partner and localizer of BRCA2 isoform X1 XP_011544248.1:p....

XP_011544248.1:p.Pro390=

XP_011544248.1:p....

XP_011544248.1:p.Pro390fs

XP_011544248.1:p....

XP_011544248.1:p.Pro390fs

partner and localizer of BRCA2 isoform X4 XP_011544249.1:p....

XP_011544249.1:p.Pro390=

XP_011544249.1:p....

XP_011544249.1:p.Pro390fs

XP_011544249.1:p....

XP_011544249.1:p.Pro390fs

partner and localizer of BRCA2 isoform X6 XP_011544250.1:p....

XP_011544250.1:p.Pro93=

XP_011544250.1:p....

XP_011544250.1:p.Pro93fs

XP_011544250.1:p....

XP_011544250.1:p.Pro93fs

partner and localizer of BRCA2 isoform X2 XP_016879160.1:p....

XP_016879160.1:p.Pro390=

XP_016879160.1:p....

XP_016879160.1:p.Pro390fs

XP_016879160.1:p....

XP_016879160.1:p.Pro390fs

partner and localizer of BRCA2 isoform X5 XP_016879162.1:p....

XP_016879162.1:p.Pro388=

XP_016879162.1:p....

XP_016879162.1:p.Pro388fs

XP_016879162.1:p....

XP_016879162.1:p.Pro388fs

partner and localizer of BRCA2 isoform X3 XP_016879161.1:p....

XP_016879161.1:p.Pro388=

XP_016879161.1:p....

XP_016879161.1:p.Pro388fs

XP_016879161.1:p....

XP_016879161.1:p.Pro388fs

Help

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

2 SubSNP, 4 ClinVar submissions
No Submitter Submission ID Date (Build)
1 CLINVAR ss1985400989 Mar 31, 2016 (147)
2 CLINVAR ss2137523961 Jul 20, 2018 (151)
3 ClinVar RCV000210113.1 Jul 20, 2018 (151)
4 ClinVar RCV000479016.1 Jul 20, 2018 (151)
5 ClinVar RCV000568264.1 Jul 20, 2018 (151)
6 ClinVar RCV000635719.1 Jul 20, 2018 (151)
Help

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
RCV000210113.1, ss1985400989 NC_000016.10:23635382:delG NC_000016.10:23635382:delG (self)
ss2137523961 NC_000016.10:23635382:insG NC_000016.10:23635382:dupG
RCV000479016.1, RCV000568264.1, RCV000635719.1 NC_000016.10:23635382:dupG NC_000016.10:23635382:dupG
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

1 citation for rs869312772
PMID Title Author Year Journal
26845104 Improving performance of multigene panels for genomic analysis of cancer predisposition. Shirts BH et al. 2016 Genetics in medicine

Genomic regions, transcripts, and products
Top Help

NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

Software version is: 0.1.4.post833+d3ba21e