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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs184840753

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr22:35084414 (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=0.000121 (32/264690, TOPMED)
A=0.000131 (33/251104, GnomAD_exome)
A=0.000130 (25/192502, ALFA) (+ 6 more)
A=0.000121 (17/140288, GnomAD)
A=0.000166 (20/120724, ExAC)
A=0.00008 (6/78692, PAGE_STUDY)
A=0.00008 (1/13006, GO-ESP)
A=0.0005 (3/6404, 1000G_30x)
A=0.0004 (2/5008, 1000G)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ISX : 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 208902 G=0.999876 A=0.000124
European Sub 173778 G=0.999885 A=0.000115
African Sub 9744 G=0.9999 A=0.0001
African Others Sub 360 G=1.000 A=0.000
African American Sub 9384 G=0.9999 A=0.0001
Asian Sub 6348 G=0.9997 A=0.0003
East Asian Sub 4502 G=0.9996 A=0.0004
Other Asian Sub 1846 G=1.0000 A=0.0000
Latin American 1 Sub 796 G=0.999 A=0.001
Latin American 2 Sub 968 G=1.000 A=0.000
South Asian Sub 280 G=1.000 A=0.000
Other Sub 16988 G=0.99988 A=0.00012


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=0.999879 A=0.000121
gnomAD - Exomes Global Study-wide 251104 G=0.999869 A=0.000131
gnomAD - Exomes European Sub 135230 G=0.999889 A=0.000111
gnomAD - Exomes Asian Sub 48952 G=0.99978 A=0.00022
gnomAD - Exomes American Sub 34478 G=0.99985 A=0.00015
gnomAD - Exomes African Sub 16248 G=0.99994 A=0.00006
gnomAD - Exomes Ashkenazi Jewish Sub 10068 G=1.00000 A=0.00000
gnomAD - Exomes Other Sub 6128 G=0.9998 A=0.0002
Allele Frequency Aggregator Total Global 192502 G=0.999870 A=0.000130
Allele Frequency Aggregator European Sub 163648 G=0.999878 A=0.000122
Allele Frequency Aggregator Other Sub 15556 G=0.99987 A=0.00013
Allele Frequency Aggregator Asian Sub 6348 G=0.9997 A=0.0003
Allele Frequency Aggregator African Sub 4906 G=1.0000 A=0.0000
Allele Frequency Aggregator Latin American 2 Sub 968 G=1.000 A=0.000
Allele Frequency Aggregator Latin American 1 Sub 796 G=0.999 A=0.001
Allele Frequency Aggregator South Asian Sub 280 G=1.000 A=0.000
gnomAD - Genomes Global Study-wide 140288 G=0.999879 A=0.000121
gnomAD - Genomes European Sub 75968 G=0.99991 A=0.00009
gnomAD - Genomes African Sub 42054 G=0.99990 A=0.00010
gnomAD - Genomes American Sub 13660 G=0.99971 A=0.00029
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3132 G=0.9994 A=0.0006
gnomAD - Genomes Other Sub 2150 G=1.0000 A=0.0000
ExAC Global Study-wide 120724 G=0.999834 A=0.000166
ExAC Europe Sub 73070 G=0.99988 A=0.00012
ExAC Asian Sub 24836 G=0.99968 A=0.00032
ExAC American Sub 11534 G=0.99983 A=0.00017
ExAC African Sub 10380 G=1.00000 A=0.00000
ExAC Other Sub 904 G=0.999 A=0.001
The PAGE Study Global Study-wide 78692 G=0.99992 A=0.00008
The PAGE Study AfricanAmerican Sub 32510 G=0.99991 A=0.00009
The PAGE Study Mexican Sub 10810 G=0.99991 A=0.00009
The PAGE Study Asian Sub 8316 G=1.0000 A=0.0000
The PAGE Study PuertoRican Sub 7916 G=1.0000 A=0.0000
The PAGE Study NativeHawaiian Sub 4534 G=1.0000 A=0.0000
The PAGE Study Cuban Sub 4230 G=1.0000 A=0.0000
The PAGE Study Dominican Sub 3828 G=0.9997 A=0.0003
The PAGE Study CentralAmerican Sub 2450 G=1.0000 A=0.0000
The PAGE Study SouthAmerican Sub 1982 G=0.9995 A=0.0005
The PAGE Study NativeAmerican Sub 1260 G=1.0000 A=0.0000
The PAGE Study SouthAsian Sub 856 G=1.000 A=0.000
GO Exome Sequencing Project Global Study-wide 13006 G=0.99992 A=0.00008
GO Exome Sequencing Project European American Sub 8600 G=0.9999 A=0.0001
GO Exome Sequencing Project African American Sub 4406 G=1.0000 A=0.0000
1000Genomes_30x Global Study-wide 6404 G=0.9995 A=0.0005
1000Genomes_30x African Sub 1786 G=1.0000 A=0.0000
1000Genomes_30x Europe Sub 1266 G=1.0000 A=0.0000
1000Genomes_30x South Asian Sub 1202 G=1.0000 A=0.0000
1000Genomes_30x East Asian Sub 1170 G=0.9991 A=0.0009
1000Genomes_30x American Sub 980 G=0.998 A=0.002
1000Genomes Global Study-wide 5008 G=0.9996 A=0.0004
1000Genomes African Sub 1322 G=1.0000 A=0.0000
1000Genomes East Asian Sub 1008 G=0.9990 A=0.0010
1000Genomes Europe Sub 1006 G=1.0000 A=0.0000
1000Genomes South Asian Sub 978 G=1.000 A=0.000
1000Genomes American Sub 694 G=0.999 A=0.001
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 22 NC_000022.11:g.35084414G>A
GRCh37.p13 chr 22 NC_000022.10:g.35480407G>A
Gene: ISX, intestine specific homeobox (plus strand)
Molecule type Change Amino acid[Codon] SO Term
ISX transcript NM_001303508.2:c.413G>A R [CGG] > Q [CAG] Coding Sequence Variant
intestine-specific homeobox NP_001290437.1:p.Arg138Gln R (Arg) > Q (Gln) Missense Variant
ISX transcript variant X1 XM_047441598.1:c.413G>A R [CGG] > Q [CAG] Coding Sequence Variant
intestine-specific homeobox isoform X1 XP_047297554.1:p.Arg138Gln R (Arg) > Q (Gln) 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.

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
GRCh38.p14 chr 22 NC_000022.11:g.35084414= NC_000022.11:g.35084414G>A
GRCh37.p13 chr 22 NC_000022.10:g.35480407= NC_000022.10:g.35480407G>A
ISX transcript NM_001303508.2:c.413= NM_001303508.2:c.413G>A
ISX transcript NM_001303508.1:c.413= NM_001303508.1:c.413G>A
ISX transcript variant X1 XM_047441598.1:c.413= XM_047441598.1:c.413G>A
ISX transcript NM_001008494.1:c.413= NM_001008494.1:c.413G>A
intestine-specific homeobox NP_001290437.1:p.Arg138= NP_001290437.1:p.Arg138Gln
intestine-specific homeobox isoform X1 XP_047297554.1:p.Arg138= XP_047297554.1:p.Arg138Gln
intestine-specific homeobox NP_001008494.1:p.Arg138= NP_001008494.1:p.Arg138Gln
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#.

40 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss466174920 Sep 17, 2011 (135)
2 1000GENOMES ss491191783 May 04, 2012 (137)
3 EXOME_CHIP ss491570914 May 04, 2012 (137)
4 NHLBI-ESP ss713622088 Apr 25, 2013 (138)
5 ILLUMINA ss780762005 Sep 08, 2015 (146)
6 ILLUMINA ss783441021 Sep 08, 2015 (146)
7 1000GENOMES ss1367131816 Aug 21, 2014 (142)
8 EVA_EXAC ss1694321476 Apr 01, 2015 (144)
9 ILLUMINA ss1752420169 Sep 08, 2015 (146)
10 ILLUMINA ss1917955339 Feb 12, 2016 (147)
11 ILLUMINA ss1946589022 Feb 12, 2016 (147)
12 ILLUMINA ss1959978079 Feb 12, 2016 (147)
13 HUMAN_LONGEVITY ss2247261115 Dec 20, 2016 (150)
14 GNOMAD ss2745103005 Nov 08, 2017 (151)
15 GNOMAD ss2750544258 Nov 08, 2017 (151)
16 GNOMAD ss2974292249 Nov 08, 2017 (151)
17 ILLUMINA ss3022184909 Nov 08, 2017 (151)
18 ILLUMINA ss3628532043 Oct 12, 2018 (152)
19 ILLUMINA ss3634867230 Oct 12, 2018 (152)
20 ILLUMINA ss3640574534 Oct 12, 2018 (152)
21 ILLUMINA ss3644799957 Oct 12, 2018 (152)
22 ILLUMINA ss3652648232 Oct 12, 2018 (152)
23 ILLUMINA ss3725967563 Jul 13, 2019 (153)
24 ILLUMINA ss3744502489 Jul 13, 2019 (153)
25 ILLUMINA ss3745167082 Jul 13, 2019 (153)
26 EVA ss3759373170 Jul 13, 2019 (153)
27 PAGE_CC ss3772090499 Jul 13, 2019 (153)
28 ILLUMINA ss3772662991 Jul 13, 2019 (153)
29 MOLMED_UU ss3798737051 Jul 13, 2019 (153)
30 EVA ss3825442224 Apr 27, 2020 (154)
31 EVA ss3825969942 Apr 27, 2020 (154)
32 EVA ss3986861503 Apr 26, 2021 (155)
33 TOPMED ss5108942069 Apr 26, 2021 (155)
34 1000G_HIGH_COVERAGE ss5311072927 Oct 16, 2022 (156)
35 EVA ss5441250545 Oct 16, 2022 (156)
36 1000G_HIGH_COVERAGE ss5618615955 Oct 16, 2022 (156)
37 EVA ss5822061341 Oct 16, 2022 (156)
38 EVA ss5847943916 Oct 16, 2022 (156)
39 EVA ss5881789822 Oct 16, 2022 (156)
40 EVA ss5959333777 Oct 16, 2022 (156)
41 1000Genomes NC_000022.10 - 35480407 Oct 12, 2018 (152)
42 1000Genomes_30x NC_000022.11 - 35084414 Oct 16, 2022 (156)
43 ExAC NC_000022.10 - 35480407 Oct 12, 2018 (152)
44 gnomAD - Genomes NC_000022.11 - 35084414 Apr 26, 2021 (155)
45 gnomAD - Exomes NC_000022.10 - 35480407 Jul 13, 2019 (153)
46 GO Exome Sequencing Project NC_000022.10 - 35480407 Oct 12, 2018 (152)
47 The PAGE Study NC_000022.11 - 35084414 Jul 13, 2019 (153)
48 TopMed NC_000022.11 - 35084414 Apr 26, 2021 (155)
49 ALFA NC_000022.11 - 35084414 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
80682742, 5900711, 14434118, 1899056, ss466174920, ss491191783, ss491570914, ss713622088, ss780762005, ss783441021, ss1367131816, ss1694321476, ss1752420169, ss1917955339, ss1946589022, ss1959978079, ss2745103005, ss2750544258, ss2974292249, ss3022184909, ss3628532043, ss3634867230, ss3640574534, ss3644799957, ss3652648232, ss3744502489, ss3745167082, ss3759373170, ss3772662991, ss3798737051, ss3825442224, ss3825969942, ss3986861503, ss5441250545, ss5822061341, ss5847943916, ss5959333777 NC_000022.10:35480406:G:A NC_000022.11:35084413:G:A (self)
106141890, 569746167, 1311968, 384051016, 11711104679, ss2247261115, ss3725967563, ss3772090499, ss5108942069, ss5311072927, ss5618615955, ss5881789822 NC_000022.11:35084413:G:A NC_000022.11:35084413: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 rs184840753

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