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dbSNP Short Genetic Variations

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.

rs6440

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr8:142917854 (GRCh38.p12) 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>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.00097 (238/244402, GnomAD)
G=0.00436 (548/125568, TOPMED)
G=0.00116 (140/121138, ExAC) (+ 5 more)
G=0.0036 (111/30966, GnomAD)
G=0.0033 (43/13006, GO-ESP)
G=0.002 (11/5008, 1000G)
G=0.000 (0/3854, ALSPAC)
G=0.000 (1/3708, TWINSUK)
Clinical Significance
Reported in ClinVar
Gene : Consequence
CYP11B2 : 2KB Upstream Variant
Publications
0 citations
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.p12 chr 8 NC_000008.11:g.142917854C>G
GRCh37.p13 chr 8 NC_000008.10:g.143999270C>G
LOC106799834 genomic region NG_046133.1:g.14497C>G
CYP11B2 RefSeqGene NG_008374.1:g.4990G>C
LOC110673971 genomic region NG_055453.1:g.113C>G
Gene: CYP11B2, cytochrome P450 family 11 subfamily B member 2 (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
CYP11B2 transcript NM_000498.3:c. N/A Upstream 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.

Allele: G (allele ID: 353825 )
ClinVar Accession Disease Names Clinical Significance
RCV000291813.1 Corticosterone methyloxidase type 2 deficiency Likely-Benign
RCV000345330.1 Hyperaldosteronism, familial, type I Likely-Benign
RCV000381522.1 Corticosterone methyloxidase type 1 deficiency Likely-Benign
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 - Exomes Global Study-wide 244402 C=0.99903 G=0.00097
gnomAD - Exomes European Sub 132210 C=0.99989 G=0.00011
gnomAD - Exomes Asian Sub 48024 C=0.9999 G=0.0001
gnomAD - Exomes American Sub 33576 C=0.9993 G=0.0007
gnomAD - Exomes African Sub 15286 C=0.9877 G=0.0123
gnomAD - Exomes Ashkenazi Jewish Sub 9840 C=1.000 G=0.000
gnomAD - Exomes Other Sub 5466 C=0.999 G=0.001
TopMed Global Study-wide 125568 C=0.99564 G=0.00436
ExAC Global Study-wide 121138 C=0.99884 G=0.00116
ExAC Europe Sub 73180 C=0.9999 G=0.0001
ExAC Asian Sub 25136 C=1.0000 G=0.0000
ExAC American Sub 11562 C=0.9993 G=0.0007
ExAC African Sub 10354 C=0.9883 G=0.0117
ExAC Other Sub 906 C=1.00 G=0.00
gnomAD - Genomes Global Study-wide 30966 C=0.9964 G=0.0036
gnomAD - Genomes European Sub 18502 C=0.9998 G=0.0002
gnomAD - Genomes African Sub 8722 C=0.988 G=0.012
gnomAD - Genomes East Asian Sub 1622 C=1.000 G=0.000
gnomAD - Genomes Other Sub 980 C=1.00 G=0.00
gnomAD - Genomes American Sub 838 C=1.00 G=0.00
gnomAD - Genomes Ashkenazi Jewish Sub 302 C=1.00 G=0.00
GO Exome Sequencing Project Global Study-wide 13006 C=0.9967 G=0.0033
GO Exome Sequencing Project European American Sub 8600 C=1.000 G=0.000
GO Exome Sequencing Project African American Sub 4406 C=0.990 G=0.010
1000Genomes Global Study-wide 5008 C=0.998 G=0.002
1000Genomes African Sub 1322 C=0.992 G=0.008
1000Genomes East Asian Sub 1008 C=1.000 G=0.000
1000Genomes Europe Sub 1006 C=1.000 G=0.000
1000Genomes South Asian Sub 978 C=1.00 G=0.00
1000Genomes American Sub 694 C=1.00 G=0.00
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=1.000 G=0.000
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=1.000 G=0.000
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= G Note
GRCh38.p12 chr 8 NC_000008.11:g.142917854C= NC_000008.11:g.14291785...

NC_000008.11:g.142917854C>G

GRCh37.p13 chr 8 NC_000008.10:g.143999270C= NC_000008.10:g.14399927...

NC_000008.10:g.143999270C>G

LOC106799834 genomic region NG_046133.1:g.14497C= NG_046133.1:g.14497C>G
CYP11B2 RefSeqGene NG_008374.1:g.4990G= NG_008374.1:g.4990G>C
LOC110673971 genomic region NG_055453.1:g.113C= NG_055453.1:g.113C>G
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#.

21 SubSNP, 8 Frequency, 3 ClinVar submissions
No Submitter Submission ID Date (Build)
1 WIAF-CSNP ss8086 Sep 19, 2000 (52)
2 BUSHMAN ss199936052 Jul 04, 2010 (132)
3 1000GENOMES ss224053136 Jul 14, 2010 (132)
4 1000GENOMES ss490971969 May 04, 2012 (137)
5 ILLUMINA ss534509624 Sep 08, 2015 (146)
6 TISHKOFF ss561154183 Apr 25, 2013 (138)
7 NHLBI-ESP ss712861424 Apr 25, 2013 (138)
8 JMKIDD_LAB ss1067500751 Aug 21, 2014 (142)
9 JMKIDD_LAB ss1076014182 Aug 21, 2014 (142)
10 1000GENOMES ss1332398745 Aug 21, 2014 (142)
11 EVA_UK10K_ALSPAC ss1621996328 Apr 01, 2015 (144)
12 EVA_UK10K_TWINSUK ss1664990361 Apr 01, 2015 (144)
13 EVA_EXAC ss1689344415 Apr 01, 2015 (144)
14 HAMMER_LAB ss1805821048 Sep 08, 2015 (146)
15 WEILL_CORNELL_DGM ss1929458872 Feb 12, 2016 (147)
16 TOPMED ss2478353637 Dec 20, 2016 (150)
17 GNOMAD ss2737388916 Nov 08, 2017 (151)
18 GNOMAD ss2748117804 Nov 08, 2017 (151)
19 GNOMAD ss2874030619 Nov 08, 2017 (151)
20 TOPMED ss3578795733 Nov 08, 2017 (151)
21 ILLUMINA ss3630185771 Oct 12, 2018 (152)
22 1000Genomes NC_000008.10 - 143999270 Oct 12, 2018 (152)
23 The Avon Longitudinal Study of Parents and Children NC_000008.10 - 143999270 Oct 12, 2018 (152)
24 ExAC NC_000008.10 - 143999270 Oct 12, 2018 (152)
25 gnomAD - Genomes NC_000008.10 - 143999270 Oct 12, 2018 (152)
26 gnomAD - Exomes NC_000008.10 - 143999270 Oct 12, 2018 (152)
27 GO Exome Sequencing Project NC_000008.10 - 143999270 Oct 12, 2018 (152)
28 TopMed NC_000008.11 - 142917854 Oct 12, 2018 (152)
29 UK 10K study - Twins NC_000008.10 - 143999270 Oct 12, 2018 (152)
30 ClinVar RCV000291813.1 Oct 12, 2018 (152)
31 ClinVar RCV000345330.1 Oct 12, 2018 (152)
32 ClinVar RCV000381522.1 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).

Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss199936052 NC_000008.9:143996271:C:G NC_000008.11:142917853:C:G (self)
44613331, 24833958, 9457069, 214658373, 5212138, 858556, 24833958, ss224053136, ss490971969, ss534509624, ss561154183, ss712861424, ss1067500751, ss1076014182, ss1332398745, ss1621996328, ss1664990361, ss1689344415, ss1805821048, ss1929458872, ss2478353637, ss2737388916, ss2748117804, ss2874030619, ss3630185771 NC_000008.10:143999269:C:G NC_000008.11:142917853:C:G (self)
RCV000291813.1, RCV000345330.1, RCV000381522.1, 403298000, ss3578795733 NC_000008.11:142917853:C:G NC_000008.11:142917853:C:G (self)
ss8086 NT_008046.16:57272818:C:G NC_000008.11:142917853:C: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 rs6440

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.post104+4a6ee9c