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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS 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.

rs1469659078

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr14:21057952-21057953 (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
delG
Variation Type
Indel Insertion and Deletion
Frequency
delG=0.000004 (1/264690, TOPMED)
delG=0.000007 (1/140106, GnomAD)
delG=0.00000 (0/14050, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
RNASE8 : Frameshift Variant
NDRG2 : Intron Variant
Publications
0 citations
Genomic View
See rs on genome

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20231103111315
Population Group Sample Size Ref Allele Alt Allele Ref HMOZ Alt HMOZ HTRZ HWEP
Total Global 14050 GG=1.00000 G=0.00000 1.0 0.0 0.0 N/A
European Sub 9690 GG=1.0000 G=0.0000 1.0 0.0 0.0 N/A
African Sub 2898 GG=1.0000 G=0.0000 1.0 0.0 0.0 N/A
African Others Sub 114 GG=1.000 G=0.000 1.0 0.0 0.0 N/A
African American Sub 2784 GG=1.0000 G=0.0000 1.0 0.0 0.0 N/A
Asian Sub 112 GG=1.000 G=0.000 1.0 0.0 0.0 N/A
East Asian Sub 86 GG=1.00 G=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 26 GG=1.00 G=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 GG=1.000 G=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 GG=1.000 G=0.000 1.0 0.0 0.0 N/A
South Asian Sub 98 GG=1.00 G=0.00 1.0 0.0 0.0 N/A
Other Sub 496 GG=1.000 G=0.000 1.0 0.0 0.0 N/A


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").

Download
Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 264690 GG=0.999996 delG=0.000004
gnomAD - Genomes Global Study-wide 140106 GG=0.999993 delG=0.000007
gnomAD - Genomes European Sub 75908 GG=0.99999 delG=0.00001
gnomAD - Genomes African Sub 41964 GG=1.00000 delG=0.00000
gnomAD - Genomes American Sub 13628 GG=1.00000 delG=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3320 GG=1.0000 delG=0.0000
gnomAD - Genomes East Asian Sub 3134 GG=1.0000 delG=0.0000
gnomAD - Genomes Other Sub 2152 GG=1.0000 delG=0.0000
Allele Frequency Aggregator Total Global 14050 GG=1.00000 delG=0.00000
Allele Frequency Aggregator European Sub 9690 GG=1.0000 delG=0.0000
Allele Frequency Aggregator African Sub 2898 GG=1.0000 delG=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 GG=1.000 delG=0.000
Allele Frequency Aggregator Other Sub 496 GG=1.000 delG=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 GG=1.000 delG=0.000
Allele Frequency Aggregator Asian Sub 112 GG=1.000 delG=0.000
Allele Frequency Aggregator South Asian Sub 98 GG=1.00 delG=0.00
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.p14 chr 14 NC_000014.9:g.21057953del
GRCh37.p13 chr 14 NC_000014.8:g.21526112del
Gene: NDRG2, NDRG family member 2 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
NDRG2 transcript variant 9 NM_001282211.2:c.24+12876…

NM_001282211.2:c.24+12876del

 		N/A Intron Variant
NDRG2 transcript variant 10 NM_001282212.2:c. N/A Genic Upstream Transcript Variant
NDRG2 transcript variant 11 NM_001282213.2:c. N/A Genic Upstream Transcript Variant
NDRG2 transcript variant 12 NM_001282214.2:c. N/A Genic Upstream Transcript Variant
NDRG2 transcript variant 13 NM_001282215.2:c. N/A Genic Upstream Transcript Variant
NDRG2 transcript variant 14 NM_001282216.2:c. N/A Genic Upstream Transcript Variant
NDRG2 transcript variant 15 NM_001320329.2:c. N/A Genic Upstream Transcript Variant
NDRG2 transcript variant 16 NM_001354558.2:c. N/A Genic Upstream Transcript Variant
NDRG2 transcript variant 17 NM_001354559.2:c. N/A Genic Upstream Transcript Variant
NDRG2 transcript variant 18 NM_001354560.2:c. N/A Genic Upstream Transcript Variant
NDRG2 transcript variant 19 NM_001354561.2:c. N/A Genic Upstream Transcript Variant
NDRG2 transcript variant 20 NM_001354562.2:c. N/A Genic Upstream Transcript Variant
NDRG2 transcript variant 21 NM_001354564.2:c. N/A Genic Upstream Transcript Variant
NDRG2 transcript variant 22 NM_001354565.2:c. N/A Genic Upstream Transcript Variant
NDRG2 transcript variant 23 NM_001354566.1:c. N/A Genic Upstream Transcript Variant
NDRG2 transcript variant 24 NM_001354567.2:c. N/A Genic Upstream Transcript Variant
NDRG2 transcript variant 25 NM_001354568.2:c. N/A Genic Upstream Transcript Variant
NDRG2 transcript variant 26 NM_001354569.1:c. N/A Genic Upstream Transcript Variant
NDRG2 transcript variant 27 NM_001354570.2:c. N/A Genic Upstream Transcript Variant
NDRG2 transcript variant 2 NM_016250.3:c. N/A Genic Upstream Transcript Variant
NDRG2 transcript variant 1 NM_201535.2:c. N/A Genic Upstream Transcript Variant
NDRG2 transcript variant 3 NM_201536.2:c. N/A Genic Upstream Transcript Variant
NDRG2 transcript variant 4 NM_201537.2:c. N/A Genic Upstream Transcript Variant
NDRG2 transcript variant 5 NM_201538.2:c. N/A Genic Upstream Transcript Variant
NDRG2 transcript variant 6 NM_201539.2:c. N/A Genic Upstream Transcript Variant
NDRG2 transcript variant 7 NM_201540.2:c. N/A Genic Upstream Transcript Variant
NDRG2 transcript variant 8 NM_201541.2:c. N/A Genic Upstream Transcript Variant
Gene: RNASE8, ribonuclease A family member 8 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
RNASE8 transcript NM_138331.2:c.61del A [GCA] > Q [CA] Coding Sequence Variant
ribonuclease 8 precursor NP_612204.1:p.Ala21fs A (Ala) > Q (Gln) Frameshift Variant
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.

Not Reported in ClinVar
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
GRCh38.p14 chr 14 NC_000014.9:g.21057952_21057953= NC_000014.9:g.21057953del
GRCh37.p13 chr 14 NC_000014.8:g.21526111_21526112= NC_000014.8:g.21526112del
RNASE8 transcript NM_138331.2:c.60_61= NM_138331.2:c.61del
RNASE8 transcript NM_138331.1:c.60_61= NM_138331.1:c.61del
ribonuclease 8 precursor NP_612204.1:p.Val20_Ala21= NP_612204.1:p.Ala21fs
NDRG2 transcript variant 9 NM_001282211.2:c.24+12876= NM_001282211.2:c.24+12876del
NDRG2 transcript variant X15 XM_005267906.1:c.24+12876= XM_005267906.1:c.24+12876del
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, 3 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss4274204345 Apr 26, 2021 (155)
2 TOPMED ss4962998233 Apr 26, 2021 (155)
3 gnomAD - Genomes NC_000014.9 - 21057952 Apr 26, 2021 (155)
4 TopMed NC_000014.9 - 21057952 Apr 26, 2021 (155)
5 ALFA NC_000014.9 - 21057952 Apr 26, 2021 (155)
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
444746732, 178543892, ss4274204345, ss4962998233 NC_000014.9:21057951:G: NC_000014.9:21057951:GG:G (self)
11543054660 NC_000014.9:21057951:GG:G NC_000014.9:21057951:GG:G (self)
Help

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

No publications for rs1469659078

Help

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
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: 2.0.1.post820+afb47a3d