Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

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.

rs6087474

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr20:33307920 (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>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.405123 (107232/264690, TOPMED)
C=0.395469 (52784/133472, GnomAD)
A=0.24995 (7062/28254, 14KJPN) (+ 11 more)
C=0.37800 (6999/18516, ALFA)
A=0.25510 (4275/16758, 8.3KJPN)
A=0.4910 (2459/5008, 1000G)
C=0.3630 (1625/4476, Estonian)
A=0.2884 (845/2930, KOREAN)
C=0.087 (87/998, GoNL)
C=0.292 (175/600, NorthernSweden)
A=0.338 (131/388, SGDP_PRJ)
A=0.472 (102/216, Qatari)
A=0.27 (13/48, Siberian)
C=0.28 (11/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
BPIFB1 : Intron 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 18516 A=0.62200 C=0.37800
European Sub 14148 A=0.65430 C=0.34570
African Sub 2898 A=0.4800 C=0.5200
African Others Sub 114 A=0.482 C=0.518
African American Sub 2784 A=0.4799 C=0.5201
Asian Sub 112 A=0.277 C=0.723
East Asian Sub 86 A=0.31 C=0.69
Other Asian Sub 26 A=0.15 C=0.85
Latin American 1 Sub 146 A=0.637 C=0.363
Latin American 2 Sub 610 A=0.687 C=0.313
South Asian Sub 98 A=0.48 C=0.52
Other Sub 504 A=0.554 C=0.446


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
TopMed Global Study-wide 264690 A=0.594877 C=0.405123
gnomAD - Genomes Global Study-wide 133472 A=0.604531 C=0.395469
gnomAD - Genomes European Sub 72792 A=0.66617 C=0.33383
gnomAD - Genomes African Sub 39428 A=0.49229 C=0.50771
gnomAD - Genomes American Sub 13006 A=0.66900 C=0.33100
gnomAD - Genomes Ashkenazi Jewish Sub 3248 A=0.5557 C=0.4443
gnomAD - Genomes East Asian Sub 2948 A=0.3562 C=0.6438
gnomAD - Genomes Other Sub 2050 A=0.6000 C=0.4000
14KJPN JAPANESE Study-wide 28254 A=0.24995 C=0.75005
Allele Frequency Aggregator Total Global 18516 A=0.62200 C=0.37800
Allele Frequency Aggregator European Sub 14148 A=0.65430 C=0.34570
Allele Frequency Aggregator African Sub 2898 A=0.4800 C=0.5200
Allele Frequency Aggregator Latin American 2 Sub 610 A=0.687 C=0.313
Allele Frequency Aggregator Other Sub 504 A=0.554 C=0.446
Allele Frequency Aggregator Latin American 1 Sub 146 A=0.637 C=0.363
Allele Frequency Aggregator Asian Sub 112 A=0.277 C=0.723
Allele Frequency Aggregator South Asian Sub 98 A=0.48 C=0.52
8.3KJPN JAPANESE Study-wide 16758 A=0.25510 C=0.74490
1000Genomes Global Study-wide 5008 A=0.4910 C=0.5090
1000Genomes African Sub 1322 A=0.4539 C=0.5461
1000Genomes East Asian Sub 1008 A=0.3343 C=0.6657
1000Genomes Europe Sub 1006 A=0.6412 C=0.3588
1000Genomes South Asian Sub 978 A=0.418 C=0.582
1000Genomes American Sub 694 A=0.674 C=0.326
Genetic variation in the Estonian population Estonian Study-wide 4476 A=0.6370 C=0.3630
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.2884 C=0.7116
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.913 C=0.087
Northern Sweden ACPOP Study-wide 600 A=0.708 C=0.292
SGDP_PRJ Global Study-wide 388 A=0.338 C=0.662
Qatari Global Study-wide 216 A=0.472 C=0.528
Siberian Global Study-wide 48 A=0.27 C=0.73
The Danish reference pan genome Danish Study-wide 40 A=0.72 C=0.28
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 20 NC_000020.11:g.33307920A>C
GRCh37.p13 chr 20 NC_000020.10:g.31895726A>C
Gene: BPIFB1, BPI fold containing family B member 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
BPIFB1 transcript NM_033197.3:c.1395+933A>C N/A Intron 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= C
GRCh38.p14 chr 20 NC_000020.11:g.33307920= NC_000020.11:g.33307920A>C
GRCh37.p13 chr 20 NC_000020.10:g.31895726= NC_000020.10:g.31895726A>C
BPIFB1 transcript NM_033197.2:c.1395+933= NM_033197.2:c.1395+933A>C
BPIFB1 transcript NM_033197.3:c.1395+933= NM_033197.3:c.1395+933A>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#.

49 SubSNP, 14 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss8410391 Apr 21, 2003 (114)
2 HGSV ss82472884 Dec 14, 2007 (130)
3 BCMHGSC_JDW ss91686649 Mar 24, 2008 (129)
4 1000GENOMES ss113277760 Jan 25, 2009 (130)
5 ENSEMBL ss138236909 Dec 01, 2009 (131)
6 GMI ss156381574 Dec 01, 2009 (131)
7 COMPLETE_GENOMICS ss168067525 Jul 04, 2010 (132)
8 COMPLETE_GENOMICS ss169485052 Jul 04, 2010 (132)
9 BUSHMAN ss203875847 Jul 04, 2010 (132)
10 BL ss255609044 May 09, 2011 (134)
11 GMI ss283366272 May 04, 2012 (137)
12 TISHKOFF ss566221547 Apr 25, 2013 (138)
13 SSMP ss662103590 Apr 25, 2013 (138)
14 EVA-GONL ss994678764 Aug 21, 2014 (142)
15 1000GENOMES ss1364601864 Aug 21, 2014 (142)
16 EVA_GENOME_DK ss1579492002 Apr 01, 2015 (144)
17 HAMMER_LAB ss1809483908 Sep 08, 2015 (146)
18 WEILL_CORNELL_DGM ss1938191995 Feb 12, 2016 (147)
19 JJLAB ss2029878621 Sep 14, 2016 (149)
20 USC_VALOUEV ss2158442297 Dec 20, 2016 (150)
21 HUMAN_LONGEVITY ss2242393691 Dec 20, 2016 (150)
22 SYSTEMSBIOZJU ss2629433135 Nov 08, 2017 (151)
23 GRF ss2704132104 Nov 08, 2017 (151)
24 GNOMAD ss2966927914 Nov 08, 2017 (151)
25 SWEGEN ss3018117512 Nov 08, 2017 (151)
26 CSHL ss3352495104 Nov 08, 2017 (151)
27 URBANLAB ss3651013351 Oct 12, 2018 (152)
28 EGCUT_WGS ss3684797110 Jul 13, 2019 (153)
29 EVA_DECODE ss3706863104 Jul 13, 2019 (153)
30 ACPOP ss3743360643 Jul 13, 2019 (153)
31 PACBIO ss3788637449 Jul 13, 2019 (153)
32 PACBIO ss3793531692 Jul 13, 2019 (153)
33 PACBIO ss3798418575 Jul 13, 2019 (153)
34 KHV_HUMAN_GENOMES ss3821760485 Jul 13, 2019 (153)
35 EVA ss3835654006 Apr 27, 2020 (154)
36 EVA ss3841453501 Apr 27, 2020 (154)
37 SGDP_PRJ ss3889016726 Apr 27, 2020 (154)
38 KRGDB ss3939284391 Apr 27, 2020 (154)
39 TOPMED ss5087099324 Apr 26, 2021 (155)
40 TOMMO_GENOMICS ss5229446559 Apr 26, 2021 (155)
41 1000G_HIGH_COVERAGE ss5308649471 Oct 16, 2022 (156)
42 EVA ss5437127495 Oct 16, 2022 (156)
43 HUGCELL_USP ss5500941486 Oct 16, 2022 (156)
44 SANFORD_IMAGENETICS ss5663135052 Oct 16, 2022 (156)
45 TOMMO_GENOMICS ss5789181585 Oct 16, 2022 (156)
46 YY_MCH ss5818011628 Oct 16, 2022 (156)
47 EVA ss5845638312 Oct 16, 2022 (156)
48 EVA ss5853125083 Oct 16, 2022 (156)
49 EVA ss5923254950 Oct 16, 2022 (156)
50 1000Genomes NC_000020.10 - 31895726 Oct 12, 2018 (152)
51 Genetic variation in the Estonian population NC_000020.10 - 31895726 Oct 12, 2018 (152)
52 The Danish reference pan genome NC_000020.10 - 31895726 Apr 27, 2020 (154)
53 gnomAD - Genomes NC_000020.11 - 33307920 Apr 26, 2021 (155)
54 Genome of the Netherlands Release 5 NC_000020.10 - 31895726 Apr 27, 2020 (154)
55 KOREAN population from KRGDB NC_000020.10 - 31895726 Apr 27, 2020 (154)
56 Northern Sweden NC_000020.10 - 31895726 Jul 13, 2019 (153)
57 Qatari NC_000020.10 - 31895726 Apr 27, 2020 (154)
58 SGDP_PRJ NC_000020.10 - 31895726 Apr 27, 2020 (154)
59 Siberian NC_000020.10 - 31895726 Apr 27, 2020 (154)
60 8.3KJPN NC_000020.10 - 31895726 Apr 26, 2021 (155)
61 14KJPN NC_000020.11 - 33307920 Oct 16, 2022 (156)
62 TopMed NC_000020.11 - 33307920 Apr 26, 2021 (155)
63 ALFA NC_000020.11 - 33307920 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).

Associated ID History Updated (Build)
rs56779254 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss82472884, ss91686649, ss113277760, ss168067525, ss169485052, ss203875847, ss255609044, ss283366272 NC_000020.9:31359386:A:C NC_000020.11:33307919:A:C (self)
78059197, 30535358, 5656941, 19253443, 46461785, 16645508, 20233917, 41033706, 10958651, 87415866, ss566221547, ss662103590, ss994678764, ss1364601864, ss1579492002, ss1809483908, ss1938191995, ss2029878621, ss2158442297, ss2629433135, ss2704132104, ss2966927914, ss3018117512, ss3352495104, ss3684797110, ss3743360643, ss3788637449, ss3793531692, ss3798418575, ss3835654006, ss3841453501, ss3889016726, ss3939284391, ss5229446559, ss5437127495, ss5663135052, ss5845638312 NC_000020.10:31895725:A:C NC_000020.11:33307919:A:C (self)
550595171, 123018689, 362208269, 4178898920, ss2242393691, ss3651013351, ss3706863104, ss3821760485, ss5087099324, ss5308649471, ss5500941486, ss5789181585, ss5818011628, ss5853125083, ss5923254950 NC_000020.11:33307919:A:C NC_000020.11:33307919:A:C (self)
ss138236909, ss156381574 NT_011362.10:2091817:A:C NC_000020.11:33307919:A:C (self)
ss8410391 NT_028392.4:2062493:A:C NC_000020.11:33307919:A:C (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 rs6087474

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