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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.

rs773884586

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr11:2132078 (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
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.00009 (3/34308, GnomAD)
G=0.00075 (21/27998, 14KJPN)
G=0.00048 (8/16756, 8.3KJPN) (+ 6 more)
G=0.08397 (996/11862, ALFA)
G=0.2008 (588/2928, KOREAN)
A=0.500 (145/290, SGDP_PRJ)
G=0.500 (145/290, SGDP_PRJ)
A=0.5 (3/6, Siberian)
G=0.5 (3/6, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
INS-IGF2 : Non Coding Transcript Variant
IGF2 : 3 Prime UTR 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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 11862 A=0.91603 G=0.08397
European Sub 7618 A=0.9311 G=0.0689
African Sub 2816 A=0.8810 G=0.1190
African Others Sub 108 A=0.907 G=0.093
African American Sub 2708 A=0.8800 G=0.1200
Asian Sub 108 A=0.963 G=0.037
East Asian Sub 84 A=0.98 G=0.02
Other Asian Sub 24 A=0.92 G=0.08
Latin American 1 Sub 146 A=0.911 G=0.089
Latin American 2 Sub 610 A=0.895 G=0.105
South Asian Sub 94 A=0.96 G=0.04
Other Sub 470 A=0.891 G=0.109


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
gnomAD - Genomes Global Study-wide 34308 A=0.99991 G=0.00009
gnomAD - Genomes European Sub 21952 A=1.00000 G=0.00000
gnomAD - Genomes African Sub 5980 A=0.9998 G=0.0002
gnomAD - Genomes American Sub 3128 A=0.9997 G=0.0003
gnomAD - Genomes East Asian Sub 1684 A=0.9994 G=0.0006
gnomAD - Genomes Ashkenazi Jewish Sub 1008 A=1.0000 G=0.0000
gnomAD - Genomes Other Sub 556 A=1.000 G=0.000
14KJPN JAPANESE Study-wide 27998 A=0.99925 G=0.00075
8.3KJPN JAPANESE Study-wide 16756 A=0.99952 G=0.00048
Allele Frequency Aggregator Total Global 11862 A=0.91603 G=0.08397
Allele Frequency Aggregator European Sub 7618 A=0.9311 G=0.0689
Allele Frequency Aggregator African Sub 2816 A=0.8810 G=0.1190
Allele Frequency Aggregator Latin American 2 Sub 610 A=0.895 G=0.105
Allele Frequency Aggregator Other Sub 470 A=0.891 G=0.109
Allele Frequency Aggregator Latin American 1 Sub 146 A=0.911 G=0.089
Allele Frequency Aggregator Asian Sub 108 A=0.963 G=0.037
Allele Frequency Aggregator South Asian Sub 94 A=0.96 G=0.04
KOREAN population from KRGDB KOREAN Study-wide 2928 A=0.7992 G=0.2008
SGDP_PRJ Global Study-wide 290 A=0.500 G=0.500
Siberian Global Study-wide 6 A=0.5 G=0.5
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 11 NC_000011.10:g.2132078A>G
GRCh37.p13 chr 11 NC_000011.9:g.2153308A>G
INS-IGF2 RefSeqGene NG_050578.1:g.34132T>C
IGF2 RefSeqGene (LRG_1031) NG_008849.1:g.22526T>C
Gene: IGF2, insulin like growth factor 2 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
IGF2 transcript variant 1 NM_000612.6:c.*909= N/A 3 Prime UTR Variant
IGF2 transcript variant 3 NM_001127598.3:c.*909= N/A 3 Prime UTR Variant
IGF2 transcript variant 5 NM_001291862.3:c.*909= N/A 3 Prime UTR Variant
IGF2 transcript variant 4 NM_001291861.3:c.*909= N/A 3 Prime UTR Variant
IGF2 transcript variant 2 NM_001007139.6:c.*909= N/A 3 Prime UTR Variant
Gene: INS-IGF2, INS-IGF2 readthrough (minus strand)
Molecule type Change Amino acid[Codon] SO Term
INS-IGF2 transcript variant 2 NM_001042376.3:c. N/A Genic Downstream Transcript Variant
INS-IGF2 transcript variant 1 NR_003512.4:n.2166T>C N/A Non Coding Transcript 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 A= G
GRCh38.p14 chr 11 NC_000011.10:g.2132078= NC_000011.10:g.2132078A>G
GRCh37.p13 chr 11 NC_000011.9:g.2153308= NC_000011.9:g.2153308A>G
INS-IGF2 RefSeqGene NG_050578.1:g.34132= NG_050578.1:g.34132T>C
INS-IGF2 transcript variant 1 NR_003512.4:n.2166= NR_003512.4:n.2166T>C
INS-IGF2 transcript variant 1 NR_003512.3:n.2166= NR_003512.3:n.2166T>C
IGF2 RefSeqGene (LRG_1031) NG_008849.1:g.22526= NG_008849.1:g.22526T>C
IGF2 transcript variant 1 NM_000612.6:c.*909= NM_000612.6:c.*909T>C
IGF2 transcript variant 1 NM_000612.5:c.*909= NM_000612.5:c.*909T>C
IGF2 transcript variant 1 NM_000612.4:c.*909= NM_000612.4:c.*909T>C
IGF2 transcript variant 2 NM_001007139.6:c.*909= NM_001007139.6:c.*909T>C
IGF2 transcript variant 2 NM_001007139.5:c.*909= NM_001007139.5:c.*909T>C
IGF2 transcript variant 2 NM_001007139.4:c.*909= NM_001007139.4:c.*909T>C
IGF2 transcript variant 3 NM_001127598.3:c.*909= NM_001127598.3:c.*909T>C
IGF2 transcript variant 3 NM_001127598.2:c.*909= NM_001127598.2:c.*909T>C
IGF2 transcript variant 3 NM_001127598.1:c.*909= NM_001127598.1:c.*909T>C
IGF2 transcript variant 4 NM_001291861.3:c.*909= NM_001291861.3:c.*909T>C
IGF2 transcript variant 4 NM_001291861.2:c.*909= NM_001291861.2:c.*909T>C
IGF2 transcript variant 4 NM_001291861.1:c.*909= NM_001291861.1:c.*909T>C
IGF2 transcript variant 5 NM_001291862.3:c.*909= NM_001291862.3:c.*909T>C
IGF2 transcript variant 5 NM_001291862.2:c.*909= NM_001291862.2:c.*909T>C
IGF2 transcript variant 5 NM_001291862.1:c.*909= NM_001291862.1:c.*909T>C
INS-IGF2 transcript variant 1 NM_001042377.1:c.*1508= NM_001042377.1:c.*1508T>C
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#.

12 SubSNP, 7 Frequency submissions
No Submitter Submission ID Date (Build)
1 DDI ss1426509023 Apr 01, 2015 (144)
2 USC_VALOUEV ss2154773128 Dec 20, 2016 (150)
3 GRF ss2699038942 Nov 08, 2017 (151)
4 GNOMAD ss2895539071 Nov 08, 2017 (151)
5 URBANLAB ss3649513594 Oct 12, 2018 (152)
6 SGDP_PRJ ss3875485938 Apr 26, 2020 (154)
7 KRGDB ss3923708254 Apr 26, 2020 (154)
8 TOMMO_GENOMICS ss5200365704 Apr 26, 2021 (155)
9 EVA ss5397296814 Oct 16, 2022 (156)
10 TOMMO_GENOMICS ss5747030498 Oct 16, 2022 (156)
11 YY_MCH ss5812062601 Oct 16, 2022 (156)
12 EVA ss5836160871 Oct 16, 2022 (156)
13 gnomAD - Genomes NC_000011.10 - 2132078 Apr 26, 2021 (155)
14 KOREAN population from KRGDB NC_000011.9 - 2153308 Apr 26, 2020 (154)
15 SGDP_PRJ NC_000011.9 - 2153308 Apr 26, 2020 (154)
16 Siberian NC_000011.9 - 2153308 Apr 26, 2020 (154)
17 8.3KJPN NC_000011.9 - 2153308 Apr 26, 2021 (155)
18 14KJPN NC_000011.10 - 2132078 Oct 16, 2022 (156)
19 ALFA NC_000011.10 - 2132078 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
30885648, 27502918, 7289482, 58335011, ss1426509023, ss2154773128, ss2699038942, ss2895539071, ss3875485938, ss3923708254, ss5200365704, ss5397296814, ss5836160871 NC_000011.9:2153307:A:G NC_000011.10:2132077:A:G (self)
369390907, 80867602, 7659783733, ss3649513594, ss5747030498, ss5812062601 NC_000011.10:2132077:A:G NC_000011.10:2132077:A: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 rs773884586

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.post761+d5e8e07