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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.

rs367804502

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr5:112837704 (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
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000087 (23/264690, TOPMED)
A=0.000004 (1/250748, GnomAD_exome)
A=0.000064 (9/140252, GnomAD) (+ 5 more)
A=0.000008 (1/120838, ExAC)
A=0.00007 (2/28258, 14KJPN)
A=0.00012 (2/16760, 8.3KJPN)
A=0.00007 (1/14050, ALFA)
A=0.00008 (1/13004, GO-ESP)
Clinical Significance
Reported in ClinVar
Gene : Consequence
APC : Missense 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 30408 G=0.99993 A=0.00007
European Sub 19776 G=1.00000 A=0.00000
African Sub 7736 G=0.9999 A=0.0001
African Others Sub 298 G=1.000 A=0.000
African American Sub 7438 G=0.9999 A=0.0001
Asian Sub 112 G=1.000 A=0.000
East Asian Sub 86 G=1.00 A=0.00
Other Asian Sub 26 G=1.00 A=0.00
Latin American 1 Sub 146 G=1.000 A=0.000
Latin American 2 Sub 610 G=1.000 A=0.000
South Asian Sub 98 G=1.00 A=0.00
Other Sub 1930 G=0.9995 A=0.0005


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 G=0.999913 A=0.000087
gnomAD - Exomes Global Study-wide 250748 G=0.999996 A=0.000004
gnomAD - Exomes European Sub 134814 G=1.000000 A=0.000000
gnomAD - Exomes Asian Sub 48984 G=1.00000 A=0.00000
gnomAD - Exomes American Sub 34570 G=1.00000 A=0.00000
gnomAD - Exomes African Sub 16218 G=0.99994 A=0.00006
gnomAD - Exomes Ashkenazi Jewish Sub 10046 G=1.00000 A=0.00000
gnomAD - Exomes Other Sub 6116 G=1.0000 A=0.0000
gnomAD - Genomes Global Study-wide 140252 G=0.999936 A=0.000064
gnomAD - Genomes European Sub 75946 G=0.99999 A=0.00001
gnomAD - Genomes African Sub 42046 G=0.99983 A=0.00017
gnomAD - Genomes American Sub 13654 G=1.00000 A=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3322 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3134 G=0.9997 A=0.0003
gnomAD - Genomes Other Sub 2150 G=1.0000 A=0.0000
ExAC Global Study-wide 120838 G=0.999992 A=0.000008
ExAC Europe Sub 73050 G=1.00000 A=0.00000
ExAC Asian Sub 25078 G=1.00000 A=0.00000
ExAC American Sub 11530 G=1.00000 A=0.00000
ExAC African Sub 10274 G=0.99990 A=0.00010
ExAC Other Sub 906 G=1.000 A=0.000
14KJPN JAPANESE Study-wide 28258 G=0.99993 A=0.00007
8.3KJPN JAPANESE Study-wide 16760 G=0.99988 A=0.00012
Allele Frequency Aggregator Total Global 14050 G=0.99993 A=0.00007
Allele Frequency Aggregator European Sub 9690 G=1.0000 A=0.0000
Allele Frequency Aggregator African Sub 2898 G=1.0000 A=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 G=1.000 A=0.000
Allele Frequency Aggregator Other Sub 496 G=0.998 A=0.002
Allele Frequency Aggregator Latin American 1 Sub 146 G=1.000 A=0.000
Allele Frequency Aggregator Asian Sub 112 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 98 G=1.00 A=0.00
GO Exome Sequencing Project Global Study-wide 13004 G=0.99992 A=0.00008
GO Exome Sequencing Project European American Sub 8600 G=1.0000 A=0.0000
GO Exome Sequencing Project African American Sub 4404 G=0.9998 A=0.0002
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 5 NC_000005.10:g.112837704G>A
GRCh37.p13 chr 5 NC_000005.9:g.112173401G>A
APC RefSeqGene (LRG_130) NG_008481.4:g.150184G>A
Gene: APC, APC regulator of WNT signaling pathway (plus strand)
Molecule type Change Amino acid[Codon] SO Term
APC transcript variant 3 NM_000038.6:c.2110G>A V [GTT] > I [ATT] Coding Sequence Variant
adenomatous polyposis coli protein isoform b NP_000029.2:p.Val704Ile V (Val) > I (Ile) Missense Variant
APC transcript variant 15 NM_001354906.2:c.1261G>A V [GTT] > I [ATT] Coding Sequence Variant
adenomatous polyposis coli protein isoform m NP_001341835.1:p.Val421Ile V (Val) > I (Ile) Missense Variant
APC transcript variant 13 NM_001354904.2:c.1732G>A V [GTT] > I [ATT] Coding Sequence Variant
adenomatous polyposis coli protein isoform k NP_001341833.1:p.Val578Ile V (Val) > I (Ile) Missense Variant
APC transcript variant 6 NM_001354897.2:c.2140G>A V [GTT] > I [ATT] Coding Sequence Variant
adenomatous polyposis coli protein isoform d NP_001341826.1:p.Val714Ile V (Val) > I (Ile) Missense Variant
APC transcript variant 11 NM_001354902.2:c.1837G>A V [GTT] > I [ATT] Coding Sequence Variant
adenomatous polyposis coli protein isoform i NP_001341831.1:p.Val613Ile V (Val) > I (Ile) Missense Variant
APC transcript variant 14 NM_001354905.2:c.1630G>A V [GTT] > I [ATT] Coding Sequence Variant
adenomatous polyposis coli protein isoform l NP_001341834.1:p.Val544Ile V (Val) > I (Ile) Missense Variant
APC transcript variant 4 NM_001354895.2:c.2110G>A V [GTT] > I [ATT] Coding Sequence Variant
adenomatous polyposis coli protein isoform b NP_001341824.1:p.Val704Ile V (Val) > I (Ile) Missense Variant
APC transcript variant 7 NM_001354898.2:c.2035G>A V [GTT] > I [ATT] Coding Sequence Variant
adenomatous polyposis coli protein isoform e NP_001341827.1:p.Val679Ile V (Val) > I (Ile) Missense Variant
APC transcript variant 5 NM_001354896.2:c.2164G>A V [GTT] > I [ATT] Coding Sequence Variant
adenomatous polyposis coli protein isoform c NP_001341825.1:p.Val722Ile V (Val) > I (Ile) Missense Variant
APC transcript variant 10 NM_001354901.2:c.1933G>A V [GTT] > I [ATT] Coding Sequence Variant
adenomatous polyposis coli protein isoform h NP_001341830.1:p.Val645Ile V (Val) > I (Ile) Missense Variant
APC transcript variant 9 NM_001354900.2:c.1987G>A V [GTT] > I [ATT] Coding Sequence Variant
adenomatous polyposis coli protein isoform g NP_001341829.1:p.Val663Ile V (Val) > I (Ile) Missense Variant
APC transcript variant 8 NM_001354899.2:c.2026G>A V [GTT] > I [ATT] Coding Sequence Variant
adenomatous polyposis coli protein isoform f NP_001341828.1:p.Val676Ile V (Val) > I (Ile) Missense Variant
APC transcript variant 12 NM_001354903.2:c.1807G>A V [GTT] > I [ATT] Coding Sequence Variant
adenomatous polyposis coli protein isoform j NP_001341832.1:p.Val603Ile V (Val) > I (Ile) Missense Variant
APC transcript variant 2 NM_001127510.3:c.2110G>A V [GTT] > I [ATT] Coding Sequence Variant
adenomatous polyposis coli protein isoform b NP_001120982.1:p.Val704Ile V (Val) > I (Ile) Missense Variant
APC transcript variant 1 NM_001127511.3:c.2056G>A V [GTT] > I [ATT] Coding Sequence Variant
adenomatous polyposis coli protein isoform a NP_001120983.2:p.Val686Ile V (Val) > I (Ile) Missense 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: A (allele ID: 182357 )
ClinVar Accession Disease Names Clinical Significance
RCV000164801.5 Hereditary cancer-predisposing syndrome Uncertain-Significance
RCV000198244.6 Familial adenomatous polyposis 1 Uncertain-Significance
RCV000236550.6 not specified Uncertain-Significance
RCV000657054.3 not provided Uncertain-Significance
RCV001155352.2 APC-Associated Polyposis Disorders Uncertain-Significance
RCV002228730.1 Familial adenomatous polyposis 1 Uncertain-Significance
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
GRCh38.p14 chr 5 NC_000005.10:g.112837704= NC_000005.10:g.112837704G>A
GRCh37.p13 chr 5 NC_000005.9:g.112173401= NC_000005.9:g.112173401G>A
APC RefSeqGene (LRG_130) NG_008481.4:g.150184= NG_008481.4:g.150184G>A
APC transcript variant 3 NM_000038.6:c.2110= NM_000038.6:c.2110G>A
APC transcript variant 3 NM_000038.5:c.2110= NM_000038.5:c.2110G>A
APC transcript variant 2 NM_001127510.3:c.2110= NM_001127510.3:c.2110G>A
APC transcript variant 2 NM_001127510.2:c.2110= NM_001127510.2:c.2110G>A
APC transcript variant 1 NM_001127511.3:c.2056= NM_001127511.3:c.2056G>A
APC transcript variant 1 NM_001127511.2:c.2056= NM_001127511.2:c.2056G>A
APC transcript variant 4 NM_001354895.2:c.2110= NM_001354895.2:c.2110G>A
APC transcript variant 4 NM_001354895.1:c.2110= NM_001354895.1:c.2110G>A
APC transcript variant 6 NM_001354897.2:c.2140= NM_001354897.2:c.2140G>A
APC transcript variant 6 NM_001354897.1:c.2140= NM_001354897.1:c.2140G>A
APC transcript variant 15 NM_001354906.2:c.1261= NM_001354906.2:c.1261G>A
APC transcript variant 15 NM_001354906.1:c.1261= NM_001354906.1:c.1261G>A
APC transcript variant 5 NM_001354896.2:c.2164= NM_001354896.2:c.2164G>A
APC transcript variant 5 NM_001354896.1:c.2164= NM_001354896.1:c.2164G>A
APC transcript variant 7 NM_001354898.2:c.2035= NM_001354898.2:c.2035G>A
APC transcript variant 7 NM_001354898.1:c.2035= NM_001354898.1:c.2035G>A
APC transcript variant 8 NM_001354899.2:c.2026= NM_001354899.2:c.2026G>A
APC transcript variant 8 NM_001354899.1:c.2026= NM_001354899.1:c.2026G>A
APC transcript variant 9 NM_001354900.2:c.1987= NM_001354900.2:c.1987G>A
APC transcript variant 9 NM_001354900.1:c.1987= NM_001354900.1:c.1987G>A
APC transcript variant 11 NM_001354902.2:c.1837= NM_001354902.2:c.1837G>A
APC transcript variant 11 NM_001354902.1:c.1837= NM_001354902.1:c.1837G>A
APC transcript variant 10 NM_001354901.2:c.1933= NM_001354901.2:c.1933G>A
APC transcript variant 10 NM_001354901.1:c.1933= NM_001354901.1:c.1933G>A
APC transcript variant 12 NM_001354903.2:c.1807= NM_001354903.2:c.1807G>A
APC transcript variant 12 NM_001354903.1:c.1807= NM_001354903.1:c.1807G>A
APC transcript variant 13 NM_001354904.2:c.1732= NM_001354904.2:c.1732G>A
APC transcript variant 13 NM_001354904.1:c.1732= NM_001354904.1:c.1732G>A
APC transcript variant 14 NM_001354905.2:c.1630= NM_001354905.2:c.1630G>A
APC transcript variant 14 NM_001354905.1:c.1630= NM_001354905.1:c.1630G>A
APC transcript variant 33 NM_001407470.1:c.1261= NM_001407470.1:c.1261G>A
APC transcript variant 17 NM_001407447.1:c.2164= NM_001407447.1:c.2164G>A
APC transcript variant 22 NM_001407452.1:c.2080= NM_001407452.1:c.2080G>A
APC transcript variant 16 NM_001407446.1:c.2194= NM_001407446.1:c.2194G>A
APC transcript variant 35 NM_001407472.1:c.958= NM_001407472.1:c.958G>A
APC transcript variant 37 NR_176366.1:n.2364= NR_176366.1:n.2364G>A
APC transcript variant 18 NM_001407448.1:c.2164= NM_001407448.1:c.2164G>A
APC transcript variant 19 NM_001407449.1:c.2164= NM_001407449.1:c.2164G>A
APC transcript variant 20 NM_001407450.1:c.2110= NM_001407450.1:c.2110G>A
APC transcript variant 26 NM_001407456.1:c.1861= NM_001407456.1:c.1861G>A
APC transcript variant 30 NM_001407460.1:c.1807= NM_001407460.1:c.1807G>A
APC transcript variant 21 NM_001407451.1:c.2089= NM_001407451.1:c.2089G>A
APC transcript variant 23 NM_001407453.1:c.1933= NM_001407453.1:c.1933G>A
APC transcript variant 32 NM_001407469.1:c.1723= NM_001407469.1:c.1723G>A
APC transcript variant 34 NM_001407471.1:c.958= NM_001407471.1:c.958G>A
APC transcript variant 27 NM_001407457.1:c.1861= NM_001407457.1:c.1861G>A
APC transcript variant 25 NM_001407455.1:c.1861= NM_001407455.1:c.1861G>A
APC transcript variant 28 NM_001407458.1:c.1807= NM_001407458.1:c.1807G>A
APC transcript variant 29 NM_001407459.1:c.1807= NM_001407459.1:c.1807G>A
APC transcript variant 36 NR_176365.1:n.1945= NR_176365.1:n.1945G>A
APC transcript variant 24 NM_001407454.1:c.1861= NM_001407454.1:c.1861G>A
APC transcript variant 31 NM_001407467.1:c.1723= NM_001407467.1:c.1723G>A
adenomatous polyposis coli protein isoform b NP_000029.2:p.Val704= NP_000029.2:p.Val704Ile
adenomatous polyposis coli protein isoform b NP_001120982.1:p.Val704= NP_001120982.1:p.Val704Ile
adenomatous polyposis coli protein isoform a NP_001120983.2:p.Val686= NP_001120983.2:p.Val686Ile
adenomatous polyposis coli protein isoform b NP_001341824.1:p.Val704= NP_001341824.1:p.Val704Ile
adenomatous polyposis coli protein isoform d NP_001341826.1:p.Val714= NP_001341826.1:p.Val714Ile
adenomatous polyposis coli protein isoform m NP_001341835.1:p.Val421= NP_001341835.1:p.Val421Ile
adenomatous polyposis coli protein isoform c NP_001341825.1:p.Val722= NP_001341825.1:p.Val722Ile
adenomatous polyposis coli protein isoform e NP_001341827.1:p.Val679= NP_001341827.1:p.Val679Ile
adenomatous polyposis coli protein isoform f NP_001341828.1:p.Val676= NP_001341828.1:p.Val676Ile
adenomatous polyposis coli protein isoform g NP_001341829.1:p.Val663= NP_001341829.1:p.Val663Ile
adenomatous polyposis coli protein isoform i NP_001341831.1:p.Val613= NP_001341831.1:p.Val613Ile
adenomatous polyposis coli protein isoform h NP_001341830.1:p.Val645= NP_001341830.1:p.Val645Ile
adenomatous polyposis coli protein isoform j NP_001341832.1:p.Val603= NP_001341832.1:p.Val603Ile
adenomatous polyposis coli protein isoform k NP_001341833.1:p.Val578= NP_001341833.1:p.Val578Ile
adenomatous polyposis coli protein isoform l NP_001341834.1:p.Val544= NP_001341834.1:p.Val544Ile
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#.

12 SubSNP, 8 Frequency, 6 ClinVar submissions
No Submitter Submission ID Date (Build)
1 NHLBI-ESP ss712655627 Apr 25, 2013 (138)
2 EVA_EXAC ss1687906536 Apr 01, 2015 (144)
3 CLINVAR ss1751110662 May 21, 2015 (144)
4 HUMAN_LONGEVITY ss2276957023 Dec 20, 2016 (150)
5 GNOMAD ss2735155125 Nov 08, 2017 (151)
6 GNOMAD ss2747430718 Nov 08, 2017 (151)
7 GNOMAD ss2829156810 Nov 08, 2017 (151)
8 EVA ss3824102735 Apr 26, 2020 (154)
9 TOPMED ss4673758998 Apr 26, 2021 (155)
10 TOMMO_GENOMICS ss5173515411 Apr 26, 2021 (155)
11 TOMMO_GENOMICS ss5710415245 Oct 17, 2022 (156)
12 EVA ss5935765040 Oct 17, 2022 (156)
13 ExAC NC_000005.9 - 112173401 Oct 12, 2018 (152)
14 gnomAD - Genomes NC_000005.10 - 112837704 Apr 26, 2021 (155)
15 gnomAD - Exomes NC_000005.9 - 112173401 Jul 13, 2019 (153)
16 GO Exome Sequencing Project NC_000005.9 - 112173401 Oct 12, 2018 (152)
17 8.3KJPN NC_000005.9 - 112173401 Apr 26, 2021 (155)
18 14KJPN NC_000005.10 - 112837704 Oct 17, 2022 (156)
19 TopMed NC_000005.10 - 112837704 Apr 26, 2021 (155)
20 ALFA NC_000005.10 - 112837704 Apr 26, 2021 (155)
21 ClinVar RCV000164801.5 Oct 17, 2022 (156)
22 ClinVar RCV000198244.6 Oct 17, 2022 (156)
23 ClinVar RCV000236550.6 Oct 17, 2022 (156)
24 ClinVar RCV000657054.3 Oct 17, 2022 (156)
25 ClinVar RCV001155352.2 Oct 17, 2022 (156)
26 ClinVar RCV002228730.1 Oct 17, 2022 (156)
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
7906267, 4275932, 560854, 31484718, ss712655627, ss1687906536, ss2735155125, ss2747430718, ss2829156810, ss3824102735, ss5173515411, ss5935765040 NC_000005.9:112173400:G:A NC_000005.10:112837703:G:A (self)
RCV000164801.5, RCV000198244.6, RCV000236550.6, RCV000657054.3, RCV001155352.2, RCV002228730.1, 200249137, 44252349, 511136555, 1007962923, ss1751110662, ss2276957023, ss4673758998, ss5710415245 NC_000005.10:112837703:G:A NC_000005.10:112837703:G:A (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 rs367804502

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