rs587776405 RefSNP Report - dbSNP (original) (raw)
Welcome to the Reference SNP (rs) Report
All alleles are reported in the Forward orientation. Click on theVariant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in theHGVS tab.
Reference SNP (rs) Report
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.
Current Build 157
Released September 3, 2024
Organism
Homo sapiens
Position
chr16:23641110 (GRCh38.p14) 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
C>T
Variation Type
SNVSingle Nucleotide Variation
Frequency
None
Clinical Significance
Reported in ClinVar
Gene : Consequence
PALB2 : Synonymous Variant
DCTN5 : 2KB Upstream Variant
Publications
Genomic View
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
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.p14 chr 16 | NC_000016.10:g.23641110C>T |
| GRCh37.p13 chr 16 | NC_000016.9:g.23652431C>T |
| PALB2 RefSeqGene (LRG_308) | NG_007406.1:g.5248G>A |
Gene: DCTN5, dynactin subunit 5 (plus strand) : 2KB Upstream Variant
| Molecule type | Change | Amino acid[Codon] | SO Term |
|---|---|---|---|
| DCTN5 transcript variant 2 | NM_001199011.2:c. | N/A | Upstream Transcript Variant |
| DCTN5 transcript variant 4 | NM_001199743.2:c. | N/A | Upstream Transcript Variant |
| DCTN5 transcript variant 1 | NM_032486.4:c. | N/A | Upstream Transcript Variant |
| DCTN5 transcript variant 3 | NR_037573.2:n. | N/A | Upstream Transcript Variant |
| DCTN5 transcript variant X1 | XR_001752006.3:n. | N/A | Upstream Transcript Variant |
| DCTN5 transcript variant X2 | XR_001752007.3:n. | N/A | Upstream Transcript Variant |
Gene: PALB2, partner and localizer of BRCA2 (minus strand)
| Molecule type | Change | Amino acid[Codon] | SO Term |
|---|---|---|---|
| PALB2 transcript variant 1 | NM_024675.4:c.48G>A | K [AAG] > K [AAA] | Coding Sequence Variant |
| partner and localizer of BRCA2 isoform 1 | NP_078951.2:p.Lys16= | K (Lys) > K (Lys) | Synonymous Variant |
| PALB2 transcript variant X1 | XM_011545946.3:c. | N/A | 5 Prime UTR Variant |
| PALB2 transcript variant X2 | XM_011545947.3:c. | N/A | 5 Prime UTR Variant |
| PALB2 transcript variant X4 | XM_011545948.3:c. | N/A | 5 Prime UTR Variant |
| PALB2 transcript variant X3 | XM_017023673.3:c. | N/A | Coding Sequence Variant |
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: T (allele ID: 153708)
| ClinVar Accession | Disease Names | Clinical Significance |
|---|---|---|
| RCV000133492.2 | not provided | Pathogenic |
| RCV000566830.8 | Hereditary cancer-predisposing syndrome | Likely-Pathogenic |
| RCV001030105.9 | Familial cancer of breast | Pathogenic-Likely-Pathogenic |
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 | C= | T |
|---|---|---|
| GRCh38.p14 chr 16 | NC_000016.10:g.23641110= | NC_000016.10:g.23641110C>T |
| GRCh37.p13 chr 16 | NC_000016.9:g.23652431= | NC_000016.9:g.23652431C>T |
| PALB2 RefSeqGene (LRG_308) | NG_007406.1:g.5248= | NG_007406.1:g.5248G>A |
| PALB2 transcript variant 1 | NM_024675.4:c.48= | NM_024675.4:c.48G>A |
| PALB2 transcript | NM_024675.3:c.48= | NM_024675.3:c.48G>A |
| PALB2 transcript variant 9 | NM_001407304.1:c.-1696= | NM_001407304.1:c.-1696G>A |
| PALB2 transcript variant 15 | NM_001407310.1:c.-1696= | NM_001407310.1:c.-1696G>A |
| PALB2 transcript variant 10 | NM_001407305.1:c.-972= | NM_001407305.1:c.-972G>A |
| PALB2 transcript variant 16 | NM_001407311.1:c.-972= | NM_001407311.1:c.-972G>A |
| PALB2 transcript variant 12 | NM_001407307.1:c.-972= | NM_001407307.1:c.-972G>A |
| PALB2 transcript variant 2 | NM_001407296.1:c.48= | NM_001407296.1:c.48G>A |
| PALB2 transcript variant 3 | NM_001407297.1:c.48= | NM_001407297.1:c.48G>A |
| PALB2 transcript variant 14 | NM_001407309.1:c.-972= | NM_001407309.1:c.-972G>A |
| PALB2 transcript variant 7 | NM_001407301.1:c.48= | NM_001407301.1:c.48G>A |
| PALB2 transcript variant 4 | NM_001407298.1:c.48= | NM_001407298.1:c.48G>A |
| PALB2 transcript variant 5 | NM_001407299.1:c.48= | NM_001407299.1:c.48G>A |
| PALB2 transcript variant 6 | NM_001407300.1:c.48= | NM_001407300.1:c.48G>A |
| PALB2 transcript variant 8 | NM_001407302.1:c.48= | NM_001407302.1:c.48G>A |
| PALB2 transcript variant 17 | NM_001407312.1:c.-105= | NM_001407312.1:c.-105G>A |
| PALB2 transcript variant 18 | NM_001407313.1:c.-105= | NM_001407313.1:c.-105G>A |
| PALB2 transcript variant 19 | NM_001407314.1:c.48= | NM_001407314.1:c.48G>A |
| partner and localizer of BRCA2 isoform 1 | NP_078951.2:p.Lys16= | NP_078951.2:p.Lys16= |
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#.
1 SubSNP, 3 ClinVar submissions
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 |
|---|---|---|---|
| RCV000133492.2, RCV000566830.8, RCV001030105.9, ss1399952636 | NC_000016.10:23641109:C:T | NC_000016.10:23641109:C:T | (self) |
Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.
1 citation for rs587776405
| PMID | Title | Author | Year | Journal |
|---|---|---|---|---|
| 25099575 | Breast-cancer risk in families with mutations in PALB2. | Antoniou AC et al. | 2014 | The New England journal of medicine |
The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.
Genome context:
Select flank length:
Genomic regions, transcripts, and products
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.