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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.

rs4434890

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:202838960 (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=0.00487 (194/39822, GnomAD)
C=0.00319 (90/28256, 14KJPN)
C=0.00334 (56/16760, 8.3KJPN) (+ 6 more)
C=0.12772 (1515/11862, ALFA)
C=0.4297 (1259/2930, KOREAN)
C=0.012 (12/998, GoNL)
A=0.488 (208/426, SGDP_PRJ)
C=0.463 (100/216, Qatari)
A=0.2 (1/4, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
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 11862 A=0.87228 C=0.12772
European Sub 7618 A=0.8795 C=0.1205
African Sub 2816 A=0.8615 C=0.1385
African Others Sub 108 A=0.889 C=0.111
African American Sub 2708 A=0.8604 C=0.1396
Asian Sub 108 A=0.759 C=0.241
East Asian Sub 84 A=0.76 C=0.24
Other Asian Sub 24 A=0.75 C=0.25
Latin American 1 Sub 146 A=0.877 C=0.123
Latin American 2 Sub 610 A=0.849 C=0.151
South Asian Sub 94 A=0.83 C=0.17
Other Sub 470 A=0.883 C=0.117


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 39822 A=0.99513 C=0.00487
gnomAD - Genomes European Sub 16846 A=0.99929 C=0.00071
gnomAD - Genomes African Sub 15844 A=0.98971 C=0.01029
gnomAD - Genomes American Sub 3992 A=0.9992 C=0.0008
gnomAD - Genomes East Asian Sub 1702 A=0.9924 C=0.0076
gnomAD - Genomes Ashkenazi Jewish Sub 840 A=1.000 C=0.000
gnomAD - Genomes Other Sub 598 A=0.995 C=0.005
14KJPN JAPANESE Study-wide 28256 A=0.99681 C=0.00319
8.3KJPN JAPANESE Study-wide 16760 A=0.99666 C=0.00334
Allele Frequency Aggregator Total Global 11862 A=0.87228 C=0.12772
Allele Frequency Aggregator European Sub 7618 A=0.8795 C=0.1205
Allele Frequency Aggregator African Sub 2816 A=0.8615 C=0.1385
Allele Frequency Aggregator Latin American 2 Sub 610 A=0.849 C=0.151
Allele Frequency Aggregator Other Sub 470 A=0.883 C=0.117
Allele Frequency Aggregator Latin American 1 Sub 146 A=0.877 C=0.123
Allele Frequency Aggregator Asian Sub 108 A=0.759 C=0.241
Allele Frequency Aggregator South Asian Sub 94 A=0.83 C=0.17
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.5703 C=0.4297
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.988 C=0.012
SGDP_PRJ Global Study-wide 426 A=0.488 C=0.512
Qatari Global Study-wide 216 A=0.537 C=0.463
Siberian Global Study-wide 4 A=0.2 C=0.8
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 1 NC_000001.11:g.202838960A>C
GRCh37.p13 chr 1 NC_000001.10:g.202808088A>C
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 1 NC_000001.11:g.202838960= NC_000001.11:g.202838960A>C
GRCh37.p13 chr 1 NC_000001.10:g.202808088= NC_000001.10:g.202808088A>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#.

25 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss5943108 Feb 20, 2003 (111)
2 SC_JCM ss11196861 Jul 11, 2003 (116)
3 SSAHASNP ss35133768 May 24, 2005 (125)
4 BCMHGSC_JDW ss87938575 Mar 23, 2008 (129)
5 ENSEMBL ss138138141 Dec 01, 2009 (137)
6 1000GENOMES ss218830994 Jul 14, 2010 (137)
7 1000GENOMES ss230863491 Jul 14, 2010 (137)
8 GMI ss276179596 May 04, 2012 (137)
9 EVA-GONL ss976041439 Aug 21, 2014 (142)
10 WEILL_CORNELL_DGM ss1919268977 Feb 12, 2016 (147)
11 USC_VALOUEV ss2148182814 Dec 20, 2016 (150)
12 HUMAN_LONGEVITY ss2169301424 Dec 20, 2016 (150)
13 GRF ss2698172772 Nov 08, 2017 (151)
14 SWEGEN ss2988291200 Nov 08, 2017 (151)
15 EVA ss3747214630 Jul 12, 2019 (153)
16 SGDP_PRJ ss3850698873 Apr 25, 2020 (154)
17 KRGDB ss3895989312 Apr 25, 2020 (154)
18 GNOMAD ss4009585540 Apr 25, 2021 (155)
19 TOMMO_GENOMICS ss5147995072 Apr 25, 2021 (155)
20 1000G_HIGH_COVERAGE ss5245459600 Oct 12, 2022 (156)
21 HUGCELL_USP ss5445930207 Oct 12, 2022 (156)
22 TOMMO_GENOMICS ss5675627853 Oct 12, 2022 (156)
23 EVA ss5833127088 Oct 12, 2022 (156)
24 EVA ss5911585055 Oct 12, 2022 (156)
25 EVA ss5939086313 Oct 12, 2022 (156)
26 gnomAD - Genomes NC_000001.11 - 202838960 Apr 25, 2021 (155)
27 Genome of the Netherlands Release 5 NC_000001.10 - 202808088 Apr 25, 2020 (154)
28 KOREAN population from KRGDB NC_000001.10 - 202808088 Apr 25, 2020 (154)
29 Qatari NC_000001.10 - 202808088 Apr 25, 2020 (154)
30 SGDP_PRJ NC_000001.10 - 202808088 Apr 25, 2020 (154)
31 Siberian NC_000001.10 - 202808088 Apr 25, 2020 (154)
32 8.3KJPN NC_000001.10 - 202808088 Apr 25, 2021 (155)
33 14KJPN NC_000001.11 - 202838960 Oct 12, 2022 (156)
34 ALFA NC_000001.11 - 202838960 Apr 25, 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)
rs5780131 Oct 07, 2004 (123)
rs79321253 Jan 15, 2013 (137)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss35133768 NC_000001.8:199539744:A:C NC_000001.11:202838959:A:C (self)
ss87938575, ss276179596 NC_000001.9:201074710:A:C NC_000001.11:202838959:A:C (self)
1227292, 3166706, 1310907, 2715853, 699168, 5964379, ss218830994, ss230863491, ss976041439, ss1919268977, ss2148182814, ss2698172772, ss2988291200, ss3747214630, ss3850698873, ss3895989312, ss5147995072, ss5833127088, ss5939086313 NC_000001.10:202808087:A:C NC_000001.11:202838959:A:C (self)
36806832, 9464957, 7210352556, ss2169301424, ss4009585540, ss5245459600, ss5445930207, ss5675627853, ss5911585055 NC_000001.11:202838959:A:C NC_000001.11:202838959:A:C (self)
ss5943108, ss138138141 NT_004487.19:54296729:A:C NC_000001.11:202838959:A:C (self)
ss11196861 NT_004671.15:14163071:A:C NC_000001.11:202838959: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 rs4434890

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