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dbSNP Short Genetic Variations

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.


Current Build 155

Released April 9, 2021

Homo sapiens
chr1:796338 (GRCh38.p13) 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.

T>A / T>C / T>G
Variation Type
SNV Single Nucleotide Variation
C=0.154475 (40888/264690, TOPMED)
C=0.16038 (2688/16760, 8.3KJPN)
C=0.08389 (1342/15998, ALFA) (+ 10 more)
C=0.1544 (773/5008, 1000G)
C=0.1175 (453/3854, ALSPAC)
C=0.1206 (447/3708, TWINSUK)
C=0.1628 (477/2930, KOREAN)
C=0.1627 (298/1832, Korea1K)
C=0.140 (140/998, GoNL)
C=0.127 (76/600, NorthernSweden)
C=0.148 (32/216, Qatari)
T=0.463 (63/136, SGDP_PRJ)
C=0.03 (1/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LINC01409 : Intron Variant
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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 15998 T=0.91611 A=0.00000, C=0.08389, G=0.00000
European Sub 12636 T=0.90859 A=0.00000, C=0.09141, G=0.00000
African Sub 2108 T=0.9326 A=0.0000, C=0.0674, G=0.0000
African Others Sub 82 T=0.90 A=0.00, C=0.10, G=0.00
African American Sub 2026 T=0.9339 A=0.0000, C=0.0661, G=0.0000
Asian Sub 90 T=1.00 A=0.00, C=0.00, G=0.00
East Asian Sub 70 T=1.00 A=0.00, C=0.00, G=0.00
Other Asian Sub 20 T=1.00 A=0.00, C=0.00, G=0.00
Latin American 1 Sub 90 T=1.00 A=0.00, C=0.00, G=0.00
Latin American 2 Sub 446 T=1.000 A=0.000, C=0.000, G=0.000
South Asian Sub 74 T=1.00 A=0.00, C=0.00, G=0.00
Other Sub 554 T=0.919 A=0.000, C=0.081, G=0.000


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").

Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 264690 T=0.845525 C=0.154475
8.3KJPN JAPANESE Study-wide 16760 T=0.83962 C=0.16038
1000Genomes Global Study-wide 5008 T=0.8456 C=0.1544
1000Genomes African Sub 1322 T=0.8003 C=0.1997
1000Genomes East Asian Sub 1008 T=0.8869 C=0.1131
1000Genomes Europe Sub 1006 T=0.8867 C=0.1133
1000Genomes South Asian Sub 978 T=0.803 C=0.197
1000Genomes American Sub 694 T=0.873 C=0.127
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.8825 C=0.1175
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.8794 C=0.1206
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.8372 C=0.1628
Korean Genome Project KOREAN Study-wide 1832 T=0.8373 C=0.1627
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.860 C=0.140
Northern Sweden ACPOP Study-wide 600 T=0.873 C=0.127
Qatari Global Study-wide 216 T=0.852 C=0.148
SGDP_PRJ Global Study-wide 136 T=0.463 C=0.537
The Danish reference pan genome Danish Study-wide 40 T=0.97 C=0.03

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.p13 chr 1 NC_000001.11:g.796338T>A
GRCh38.p13 chr 1 NC_000001.11:g.796338T>C
GRCh38.p13 chr 1 NC_000001.11:g.796338T>G
GRCh37.p13 chr 1 NC_000001.10:g.731718T>A
GRCh37.p13 chr 1 NC_000001.10:g.731718T>C
GRCh37.p13 chr 1 NC_000001.10:g.731718T>G
Gene: LINC01409, uncharacterized LINC01409 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LINC01409 transcript variant X1 XR_002958522.1:n. N/A Intron Variant
LINC01409 transcript variant X5 XR_002958525.1:n. N/A Intron Variant
LINC01409 transcript variant X4 XR_946806.3:n. N/A Intron Variant
LINC01409 transcript variant X2 XR_002958523.1:n. N/A Genic Upstream Transcript Variant
LINC01409 transcript variant X3 XR_002958524.1:n. N/A Genic Upstream Transcript 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.

Not Reported in ClinVar

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 T= A C G
GRCh38.p13 chr 1 NC_000001.11:g.796338= NC_000001.11:g.796338T>A NC_000001.11:g.796338T>C NC_000001.11:g.796338T>G
GRCh37.p13 chr 1 NC_000001.10:g.731718= NC_000001.10:g.731718T>A NC_000001.10:g.731718T>C NC_000001.10:g.731718T>G

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#.

34 SubSNP, 16 Frequency submissions
No Submitter Submission ID Date (Build)
1 HGSV ss85305796 Dec 15, 2007 (129)
2 BCMHGSC_JDW ss87155524 Mar 23, 2008 (130)
3 GMI ss275680660 May 04, 2012 (144)
4 1000GENOMES ss328357240 May 09, 2011 (144)
5 SSMP ss647515956 Apr 25, 2013 (144)
6 EVA-GONL ss974769123 Aug 21, 2014 (144)
7 1000GENOMES ss1289338311 Aug 21, 2014 (144)
8 DDI ss1425684751 Apr 01, 2015 (144)
9 EVA_GENOME_DK ss1573851079 Apr 01, 2015 (144)
10 EVA_DECODE ss1584129377 Apr 01, 2015 (144)
11 EVA_UK10K_ALSPAC ss1599378251 Apr 01, 2015 (144)
12 EVA_UK10K_TWINSUK ss1642372284 Apr 01, 2015 (144)
13 WEILL_CORNELL_DGM ss1917959905 Feb 12, 2016 (147)
14 ILLUMINA ss1958229932 Feb 12, 2016 (147)
15 TOPMED ss2321501712 Dec 20, 2016 (150)
16 GRF ss2697374289 Nov 08, 2017 (151)
17 GNOMAD ss2750634657 Nov 08, 2017 (151)
18 SWEGEN ss2986148146 Nov 08, 2017 (151)
19 ILLUMINA ss3021042971 Nov 08, 2017 (151)
20 TOPMED ss3066391822 Nov 08, 2017 (151)
21 CSHL ss3343272306 Nov 08, 2017 (151)
22 ILLUMINA ss3651365024 Oct 11, 2018 (152)
23 EVA_DECODE ss3685991777 Jul 12, 2019 (153)
24 ACPOP ss3726716059 Jul 12, 2019 (153)
25 EVA ss3745720749 Jul 12, 2019 (153)
26 KHV_HUMAN_GENOMES ss3798743235 Jul 12, 2019 (153)
27 EVA ss3825981401 Apr 25, 2020 (154)
28 EVA ss3836378332 Apr 25, 2020 (154)
29 EVA ss3841782332 Apr 25, 2020 (154)
30 SGDP_PRJ ss3847994237 Apr 25, 2020 (154)
31 KRGDB ss3892834651 Apr 25, 2020 (154)
32 KOGIC ss3943628736 Apr 25, 2020 (154)
33 TOPMED ss4436425054 Apr 25, 2021 (155)
34 TOMMO_GENOMICS ss5142050191 Apr 25, 2021 (155)
35 1000Genomes NC_000001.10 - 731718 Oct 11, 2018 (152)
36 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 731718 Oct 11, 2018 (152)
37 The Danish reference pan genome NC_000001.10 - 731718 Apr 25, 2020 (154)
38 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 57115 (NC_000001.11:796337:T:A 0/140110)
Row 57116 (NC_000001.11:796337:T:C 22333/140042)
Row 57117 (NC_000001.11:796337:T:G 1/140110)

- Apr 25, 2021 (155)
39 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 57115 (NC_000001.11:796337:T:A 0/140110)
Row 57116 (NC_000001.11:796337:T:C 22333/140042)
Row 57117 (NC_000001.11:796337:T:G 1/140110)

- Apr 25, 2021 (155)
40 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 57115 (NC_000001.11:796337:T:A 0/140110)
Row 57116 (NC_000001.11:796337:T:C 22333/140042)
Row 57117 (NC_000001.11:796337:T:G 1/140110)

- Apr 25, 2021 (155)
41 Genome of the Netherlands Release 5 NC_000001.10 - 731718 Apr 25, 2020 (154)
42 KOREAN population from KRGDB NC_000001.10 - 731718 Apr 25, 2020 (154)
43 Korean Genome Project NC_000001.11 - 796338 Apr 25, 2020 (154)
44 Northern Sweden NC_000001.10 - 731718 Jul 12, 2019 (153)
45 Qatari NC_000001.10 - 731718 Apr 25, 2020 (154)
46 SGDP_PRJ NC_000001.10 - 731718 Apr 25, 2020 (154)
47 8.3KJPN NC_000001.10 - 731718 Apr 25, 2021 (155)
48 TopMed NC_000001.11 - 796338 Apr 25, 2021 (155)
49 UK 10K study - Twins NC_000001.10 - 731718 Oct 11, 2018 (152)
50 ALFA NC_000001.11 - 796338 Apr 25, 2021 (155)

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).

Associated ID History Updated (Build)
rs61770162 May 24, 2008 (130)
rs142557973 Jul 01, 2015 (144)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
7384915981 NC_000001.11:796337:T:A NC_000001.11:796337:T:A
ss85305796 NC_000001.8:771580:T:C NC_000001.11:796337:T:C (self)
ss87155524, ss275680660, ss1584129377 NC_000001.9:721580:T:C NC_000001.11:796337:T:C (self)
3000, 121, 1358313, 230, 12045, 924, 1835, 11217, 19498, 121, ss328357240, ss647515956, ss974769123, ss1289338311, ss1425684751, ss1573851079, ss1599378251, ss1642372284, ss1917959905, ss1958229932, ss2321501712, ss2697374289, ss2750634657, ss2986148146, ss3021042971, ss3343272306, ss3651365024, ss3726716059, ss3745720749, ss3825981401, ss3836378332, ss3847994237, ss3892834651, ss5142050191 NC_000001.10:731717:T:C NC_000001.11:796337:T:C (self)
6737, 12219, 31389, 7384915981, ss3066391822, ss3685991777, ss3798743235, ss3841782332, ss3943628736, ss4436425054 NC_000001.11:796337:T:C NC_000001.11:796337:T:C (self)
ss2750634657 NC_000001.10:731717:T:G NC_000001.11:796337:T:G (self)
7384915981 NC_000001.11:796337:T:G NC_000001.11:796337:T:G

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

No publications for rs58276399


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.post629+eb05767