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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.

rs6469

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr6:32040674 (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.

Alleles
C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.164937 (22256/134936, GnomAD)
T=0.21697 (17945/82708, ExAC)
T=0.18852 (4843/25690, ALFA) (+ 4 more)
T=0.18383 (3081/16760, 8.3KJPN)
T=0.1355 (394/2908, KOREAN)
T=0.155 (93/600, NorthernSweden)
C=0.494 (87/176, SGDP_PRJ)
Clinical Significance
Reported in ClinVar
Gene : Consequence
CYP21A2 : Synonymous Variant
TNXB : 500B Downstream Variant
Publications
1 citation
Genomic View
See rs on genome
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.p13 chr 6 NC_000006.12:g.32040674C>T
GRCh37.p13 chr 6 NC_000006.11:g.32008451C>T
CYP21A2 RefSeqGene (LRG_829) NG_007941.3:g.7370C>T
TNXB RefSeqGene NG_008337.2:g.73701G>A
GRCh38.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.3:g.3478996C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.2:g.3479102C>T
GRCh38.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.2:g.3282082T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.1:g.3287667T>C
GRCh38.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.2:g.3341861C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.1:g.3341159C>T
GRCh38.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.2:g.3382707C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.1:g.3388292C>T
LOC106780800 genomic region NG_045215.1:g.2903C>T
Gene: TNXB, tenascin XB (minus strand) : 500B Downstream Variant
Molecule type Change Amino acid[Codon] SO Term
TNXB transcript variant 3 NM_001365276.2:c. N/A Downstream Transcript Variant
TNXB transcript variant XB NM_019105.8:c. N/A Downstream Transcript Variant
TNXB transcript variant XB-S NM_032470.4:c. N/A Downstream Transcript Variant
Gene: CYP21A2, cytochrome P450 family 21 subfamily A member 2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
CYP21A2 transcript variant 1 NM_000500.9:c.1125C>T S [TCC] > S [TCT] Coding Sequence Variant
steroid 21-hydroxylase isoform a NP_000491.4:p.Ser375= S (Ser) > S (Ser) Synonymous Variant
CYP21A2 transcript variant 4 NM_001368144.2:c.720C>T S [TCC] > S [TCT] Coding Sequence Variant
steroid 21-hydroxylase isoform c NP_001355073.1:p.Ser240= S (Ser) > S (Ser) Synonymous Variant
CYP21A2 transcript variant 2 NM_001128590.4:c.1035C>T S [TCC] > S [TCT] Coding Sequence Variant
steroid 21-hydroxylase isoform b NP_001122062.3:p.Ser345= S (Ser) > S (Ser) Synonymous Variant
CYP21A2 transcript variant 3 NM_001368143.2:c.720C>T S [TCC] > S [TCT] Coding Sequence Variant
steroid 21-hydroxylase isoform c NP_001355072.1:p.Ser240= S (Ser) > S (Ser) Synonymous 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.

Allele: T (allele ID: 252238 )
ClinVar Accession Disease Names Clinical Significance
RCV000252555.1 not specified Benign

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 25690 C=0.81148 T=0.18852
European Sub 18276 C=0.80959 T=0.19041
African Sub 3458 C=0.8508 T=0.1492
African Others Sub 116 C=0.862 T=0.138
African American Sub 3342 C=0.8504 T=0.1496
Asian Sub 164 C=0.927 T=0.073
East Asian Sub 110 C=0.918 T=0.082
Other Asian Sub 54 C=0.94 T=0.06
Latin American 1 Sub 146 C=0.795 T=0.205
Latin American 2 Sub 610 C=0.687 T=0.313
South Asian Sub 94 C=0.80 T=0.20
Other Sub 2942 C=0.7978 T=0.2022


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 134936 C=0.835063 T=0.164937
gnomAD - Genomes European Sub 73426 C=0.83500 T=0.16500
gnomAD - Genomes African Sub 40682 C=0.86886 T=0.13114
gnomAD - Genomes American Sub 12748 C=0.74051 T=0.25949
gnomAD - Genomes East Asian Sub 3060 C=0.9020 T=0.0980
gnomAD - Genomes Ashkenazi Jewish Sub 2992 C=0.7189 T=0.2811
gnomAD - Genomes Other Sub 2028 C=0.8240 T=0.1760
ExAC Global Study-wide 82708 C=0.78303 T=0.21697
ExAC Europe Sub 47104 C=0.78518 T=0.21482
ExAC Asian Sub 19942 C=0.82514 T=0.17486
ExAC American Sub 8380 C=0.6385 T=0.3615
ExAC African Sub 6690 C=0.8226 T=0.1774
ExAC Other Sub 592 C=0.792 T=0.208
8.3KJPN JAPANESE Study-wide 16760 C=0.81617 T=0.18383
KOREAN population from KRGDB KOREAN Study-wide 2908 C=0.8645 T=0.1355
Northern Sweden ACPOP Study-wide 600 C=0.845 T=0.155
SGDP_PRJ Global Study-wide 176 C=0.494 T=0.506
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 C= T
GRCh38.p13 chr 6 NC_000006.12:g.32040674= NC_000006.12:g.32040674C>T
GRCh37.p13 chr 6 NC_000006.11:g.32008451= NC_000006.11:g.32008451C>T
CYP21A2 RefSeqGene (LRG_829) NG_007941.3:g.7370= NG_007941.3:g.7370C>T
CYP21A2 transcript variant 1 NM_000500.9:c.1125= NM_000500.9:c.1125C>T
CYP21A2 transcript variant 1 NM_000500.8:c.1125= NM_000500.8:c.1125C>T
CYP21A2 transcript variant 1 NM_000500.7:c.1125= NM_000500.7:c.1125C>T
CYP21A2 transcript variant 2 NM_001128590.4:c.1035= NM_001128590.4:c.1035C>T
CYP21A2 transcript variant 2 NM_001128590.3:c.1035= NM_001128590.3:c.1035C>T
CYP21A2 transcript variant 3 NM_001368143.2:c.720= NM_001368143.2:c.720C>T
CYP21A2 transcript variant 3 NM_001368143.1:c.720= NM_001368143.1:c.720C>T
CYP21A2 transcript variant 4 NM_001368144.2:c.720= NM_001368144.2:c.720C>T
CYP21A2 transcript variant 4 NM_001368144.1:c.720= NM_001368144.1:c.720C>T
TNXB RefSeqGene NG_008337.2:g.73701= NG_008337.2:g.73701G>A
GRCh38.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.3:g.3478996= NT_113891.3:g.3478996C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.2:g.3479102= NT_113891.2:g.3479102C>T
GRCh38.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.2:g.3282082T>C NT_167245.2:g.3282082=
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.1:g.3287667T>C NT_167245.1:g.3287667=
GRCh38.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.2:g.3341861= NT_167249.2:g.3341861C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.1:g.3341159= NT_167249.1:g.3341159C>T
GRCh38.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.2:g.3382707= NT_167247.2:g.3382707C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.1:g.3388292= NT_167247.1:g.3388292C>T
LOC106780800 genomic region NG_045215.1:g.2903= NG_045215.1:g.2903C>T
steroid 21-hydroxylase isoform a NP_000491.4:p.Ser375= NP_000491.4:p.Ser375=
steroid 21-hydroxylase isoform b NP_001122062.3:p.Ser345= NP_001122062.3:p.Ser345=
steroid 21-hydroxylase isoform c NP_001355072.1:p.Ser240= NP_001355072.1:p.Ser240=
steroid 21-hydroxylase isoform c NP_001355073.1:p.Ser240= NP_001355073.1:p.Ser240=
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#.

27 SubSNP, 7 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 WIAF-CSNP ss8120 Sep 19, 2000 (52)
2 LEE ss1540494 Oct 13, 2000 (126)
3 APPLERA_GI ss48412352 Mar 15, 2006 (130)
4 SI_MHC_SNP ss52049578 Oct 18, 2006 (130)
5 SI_MHC_SNP ss52049600 Oct 16, 2006 (130)
6 BCMHGSC_JDW ss93436921 Mar 24, 2008 (130)
7 ILLUMINA ss160629103 Dec 01, 2009 (131)
8 ILLUMINA ss481731171 Sep 08, 2015 (146)
9 CLINSEQ_SNP ss491885839 May 04, 2012 (144)
10 EVA_EXAC ss1688248292 Apr 01, 2015 (144)
11 JJLAB ss2023644106 Sep 14, 2016 (149)
12 GRF ss2707404781 Nov 08, 2017 (151)
13 GNOMAD ss2735676826 Nov 08, 2017 (151)
14 GNOMAD ss2747589633 Nov 08, 2017 (151)
15 SWEGEN ss2998801779 Nov 08, 2017 (151)
16 TOPMED ss3493920288 Nov 08, 2017 (151)
17 ILLUMINA ss3636779138 Oct 12, 2018 (152)
18 OMUKHERJEE_ADBS ss3646335457 Oct 12, 2018 (152)
19 ACPOP ss3733364583 Jul 13, 2019 (153)
20 PACBIO ss3785426409 Jul 13, 2019 (153)
21 PACBIO ss3790785597 Jul 13, 2019 (153)
22 PACBIO ss3795663112 Jul 13, 2019 (153)
23 EVA ss3838395379 Apr 26, 2020 (154)
24 EVA ss3843837546 Apr 26, 2020 (154)
25 SGDP_PRJ ss3864261317 Apr 26, 2020 (154)
26 KRGDB ss3911037995 Apr 26, 2020 (154)
27 TOMMO_GENOMICS ss5176851377 Apr 26, 2021 (155)
28 ExAC NC_000006.11 - 32008451 Oct 12, 2018 (152)
29 gnomAD - Genomes NC_000006.12 - 32040674 Apr 26, 2021 (155)
30 KOREAN population from KRGDB NC_000006.11 - 32008451 Apr 26, 2020 (154)
31 Northern Sweden NC_000006.11 - 32008451 Jul 13, 2019 (153)
32 SGDP_PRJ NC_000006.11 - 32008451 Apr 26, 2020 (154)
33 8.3KJPN NC_000006.11 - 32008451 Apr 26, 2021 (155)
34 ALFA NC_000006.12 - 32040674 Apr 26, 2021 (155)
35 ClinVar RCV000252555.1 Oct 12, 2018 (152)
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)
rs1136163 Mar 10, 2006 (126)
rs35839592 May 26, 2008 (130)
rs41316144 May 26, 2008 (130)
rs62402688 May 26, 2008 (130)
rs201005294 Jul 01, 2015 (144)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss93436921, ss491885839 NC_000006.10:32116429:C:T NC_000006.12:32040673:C:T (self)
8274840, 18215389, 6649448, 16278297, 34820684, ss481731171, ss1688248292, ss2023644106, ss2707404781, ss2735676826, ss2747589633, ss2998801779, ss3636779138, ss3646335457, ss3733364583, ss3785426409, ss3790785597, ss3795663112, ss3838395379, ss3864261317, ss3911037995, ss5176851377 NC_000006.11:32008450:C:T NC_000006.12:32040673:C:T (self)
RCV000252555.1, 221301808, 5744658685, ss3493920288, ss3843837546 NC_000006.12:32040673:C:T NC_000006.12:32040673:C:T (self)
ss8120, ss1540494, ss48412352, ss52049578, ss52049600, ss160629103 NT_007592.15:31948450:C:T NC_000006.12:32040673:C:T (self)
Help

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

1 citation for rs6469
PMID Title Author Year Journal
25741868 Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Richards S et al. 2015 Genetics in medicine
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.post596+ae089ad