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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.

rs6428619

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:91212324 (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
G>A / G>C / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.3062 (839/2740, KOREAN)
G=0.0691 (113/1636, Korea1K)
G=0.172 (74/430, SGDP_PRJ) (+ 5 more)
G=0.46 (21/46, Qatari)
A=0.00 (0/42, ALFA)
C=0.00 (0/42, ALFA)
T=0.00 (0/42, ALFA)
G=0.03 (1/36, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
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 42 G=1.00 A=0.00, C=0.00, T=0.00
European Sub 30 G=1.00 A=0.00, C=0.00, T=0.00
African Sub 8 G=1.0 A=0.0, C=0.0, T=0.0
African Others Sub 0 G=0 A=0, C=0, T=0
African American Sub 8 G=1.0 A=0.0, C=0.0, T=0.0
Asian Sub 0 G=0 A=0, C=0, T=0
East Asian Sub 0 G=0 A=0, C=0, T=0
Other Asian Sub 0 G=0 A=0, C=0, T=0
Latin American 1 Sub 2 G=1.0 A=0.0, C=0.0, T=0.0
Latin American 2 Sub 0 G=0 A=0, C=0, T=0
South Asian Sub 0 G=0 A=0, C=0, T=0
Other Sub 2 G=1.0 A=0.0, C=0.0, T=0.0


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
KOREAN population from KRGDB KOREAN Study-wide 2740 G=0.3062 C=0.6923, T=0.0015
Korean Genome Project KOREAN Study-wide 1636 G=0.0691 C=0.9309
SGDP_PRJ Global Study-wide 430 G=0.172 C=0.826, T=0.002
Qatari Global Study-wide 46 G=0.46 C=0.54
Allele Frequency Aggregator Total Global 42 G=1.00 A=0.00, C=0.00, T=0.00
Allele Frequency Aggregator European Sub 30 G=1.00 A=0.00, C=0.00, T=0.00
Allele Frequency Aggregator African Sub 8 G=1.0 A=0.0, C=0.0, T=0.0
Allele Frequency Aggregator Latin American 1 Sub 2 G=1.0 A=0.0, C=0.0, T=0.0
Allele Frequency Aggregator Other Sub 2 G=1.0 A=0.0, C=0.0, T=0.0
Allele Frequency Aggregator Latin American 2 Sub 0 G=0 A=0, C=0, T=0
Allele Frequency Aggregator South Asian Sub 0 G=0 A=0, C=0, T=0
Allele Frequency Aggregator Asian Sub 0 G=0 A=0, C=0, T=0
The Danish reference pan genome Danish Study-wide 36 G=0.03 C=0.97
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 1 NC_000001.11:g.91212324G>A
GRCh38.p14 chr 1 NC_000001.11:g.91212324G>C
GRCh38.p14 chr 1 NC_000001.11:g.91212324G>T
GRCh37.p13 chr 1 NC_000001.10:g.91677881G>A
GRCh37.p13 chr 1 NC_000001.10:g.91677881G>C
GRCh37.p13 chr 1 NC_000001.10:g.91677881G>T
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 G= A C T
GRCh38.p14 chr 1 NC_000001.11:g.91212324= NC_000001.11:g.91212324G>A NC_000001.11:g.91212324G>C NC_000001.11:g.91212324G>T
GRCh37.p13 chr 1 NC_000001.10:g.91677881= NC_000001.10:g.91677881G>A NC_000001.10:g.91677881G>C NC_000001.10:g.91677881G>T
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#.

30 SubSNP, 12 Frequency submissions
No Submitter Submission ID Date (Build)
1 BCM_SSAHASNP ss9878902 Jul 11, 2003 (116)
2 SC_JCM ss11205269 Jul 11, 2003 (116)
3 SC_JCM ss13501810 Dec 05, 2003 (126)
4 SC_SNP ss18243002 Feb 28, 2004 (123)
5 SSAHASNP ss20429224 Apr 05, 2004 (123)
6 HGSV ss77638724 Sep 08, 2015 (146)
7 HGSV ss80275404 Sep 08, 2015 (146)
8 BCM-HGSC-SUB ss205529933 Aug 21, 2014 (142)
9 GMI ss275924475 May 04, 2012 (137)
10 SSMP ss648214864 Apr 25, 2013 (138)
11 EVA_GENOME_DK ss1574227056 Apr 01, 2015 (144)
12 WEILL_CORNELL_DGM ss1918624711 Feb 12, 2016 (147)
13 GRF ss2697776492 Nov 08, 2017 (151)
14 GNOMAD ss2757983683 Nov 08, 2017 (151)
15 SWEGEN ss2987214237 Nov 08, 2017 (151)
16 CSHL ss3343569940 Nov 08, 2017 (151)
17 URBANLAB ss3646717990 Oct 11, 2018 (152)
18 PACBIO ss3783479958 Jul 12, 2019 (153)
19 PACBIO ss3789127533 Jul 12, 2019 (153)
20 PACBIO ss3794000339 Jul 12, 2019 (153)
21 SGDP_PRJ ss3849363090 Apr 25, 2020 (154)
22 KRGDB ss3894424925 Apr 25, 2020 (154)
23 KOGIC ss3944983462 Apr 25, 2020 (154)
24 TOMMO_GENOMICS ss5145055744 Apr 25, 2021 (155)
25 TOMMO_GENOMICS ss5145055745 Apr 25, 2021 (155)
26 EVA ss5320314496 Oct 12, 2022 (156)
27 SANFORD_IMAGENETICS ss5626023163 Oct 12, 2022 (156)
28 TOMMO_GENOMICS ss5670141022 Oct 12, 2022 (156)
29 TOMMO_GENOMICS ss5670141023 Oct 12, 2022 (156)
30 YY_MCH ss5800811965 Oct 12, 2022 (156)
31 The Danish reference pan genome NC_000001.10 - 91677881 Apr 25, 2020 (154)
32 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 18622000 (NC_000001.11:91212323:G:C 16123/17124)
Row 18622001 (NC_000001.11:91212323:G:T 2/17286)

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

Submission ignored due to conflicting rows:
Row 18622000 (NC_000001.11:91212323:G:C 16123/17124)
Row 18622001 (NC_000001.11:91212323:G:T 2/17286)

- Apr 25, 2021 (155)
34 KOREAN population from KRGDB NC_000001.10 - 91677881 Apr 25, 2020 (154)
35 Korean Genome Project NC_000001.11 - 91212324 Apr 25, 2020 (154)
36 Qatari NC_000001.10 - 91677881 Apr 25, 2020 (154)
37 SGDP_PRJ NC_000001.10 - 91677881 Apr 25, 2020 (154)
38 8.3KJPN

Submission ignored due to conflicting rows:
Row 3025051 (NC_000001.10:91677880:G:C 15710/16642)
Row 3025052 (NC_000001.10:91677880:G:T 7/16642)

- Apr 25, 2021 (155)
39 8.3KJPN

Submission ignored due to conflicting rows:
Row 3025051 (NC_000001.10:91677880:G:C 15710/16642)
Row 3025052 (NC_000001.10:91677880:G:T 7/16642)

- Apr 25, 2021 (155)
40 14KJPN

Submission ignored due to conflicting rows:
Row 3978126 (NC_000001.11:91212323:G:C 25717/26990)
Row 3978127 (NC_000001.11:91212323:G:T 11/26990)

- Oct 12, 2022 (156)
41 14KJPN

Submission ignored due to conflicting rows:
Row 3978126 (NC_000001.11:91212323:G:C 25717/26990)
Row 3978127 (NC_000001.11:91212323:G:T 11/26990)

- Oct 12, 2022 (156)
42 ALFA NC_000001.11 - 91212324 Apr 25, 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).

Associated ID History Updated (Build)
rs9699415 Oct 14, 2006 (127)
rs12116419 Oct 07, 2004 (123)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
9817738728 NC_000001.11:91212323:G:A NC_000001.11:91212323:G:A (self)
ss77638724, ss80275404 NC_000001.8:91389901:G:C NC_000001.11:91212323:G:C (self)
ss205529933, ss275924475 NC_000001.9:91450468:G:C NC_000001.11:91212323:G:C (self)
1605552, 1602319, 666641, 1380070, ss648214864, ss1574227056, ss1918624711, ss2697776492, ss2757983683, ss2987214237, ss3343569940, ss3783479958, ss3789127533, ss3794000339, ss3849363090, ss3894424925, ss5145055744, ss5320314496, ss5626023163 NC_000001.10:91677880:G:C NC_000001.11:91212323:G:C (self)
1361463, 9817738728, ss3646717990, ss3944983462, ss5670141022, ss5800811965 NC_000001.11:91212323:G:C NC_000001.11:91212323:G:C (self)
ss9878902, ss11205269 NT_004686.15:3552397:G:C NC_000001.11:91212323:G:C (self)
ss13501810, ss18243002, ss20429224 NT_004686.16:3552397:G:C NC_000001.11:91212323:G:C (self)
1602319, 1380070, ss2757983683, ss3849363090, ss3894424925, ss5145055745 NC_000001.10:91677880:G:T NC_000001.11:91212323:G:T (self)
9817738728, ss5670141023 NC_000001.11:91212323:G:T NC_000001.11:91212323:G:T (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 rs6428619

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