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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.

rs533127429

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr5:132331819 (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 / G>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.000004 (1/264690, TOPMED)
A=0.000080 (20/251374, GnomAD_exome)
A=0.000000 (0/140196, GnomAD) (+ 7 more)
A=0.000099 (12/121382, ExAC)
A=0.00000 (0/10680, ALFA)
C=0.00000 (0/10680, ALFA)
A=0.0002 (1/6404, 1000G_30x)
A=0.0002 (1/5008, 1000G)
C=0.0000 (0/3854, ALSPAC)
C=0.0003 (1/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SLC22A4 : Missense Variant
MIR3936HG : 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 10680 G=1.00000 A=0.00000, C=0.00000
European Sub 6962 G=1.0000 A=0.0000, C=0.0000
African Sub 2294 G=1.0000 A=0.0000, C=0.0000
African Others Sub 84 G=1.00 A=0.00, C=0.00
African American Sub 2210 G=1.0000 A=0.0000, C=0.0000
Asian Sub 108 G=1.000 A=0.000, C=0.000
East Asian Sub 84 G=1.00 A=0.00, C=0.00
Other Asian Sub 24 G=1.00 A=0.00, C=0.00
Latin American 1 Sub 146 G=1.000 A=0.000, C=0.000
Latin American 2 Sub 610 G=1.000 A=0.000, C=0.000
South Asian Sub 94 G=1.00 A=0.00, C=0.00
Other Sub 466 G=1.000 A=0.000, C=0.000


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=0.999996 C=0.000004
gnomAD - Exomes Global Study-wide 251374 G=0.999920 A=0.000080
gnomAD - Exomes European Sub 135312 G=1.000000 A=0.000000
gnomAD - Exomes Asian Sub 49010 G=0.99959 A=0.00041
gnomAD - Exomes American Sub 34576 G=1.00000 A=0.00000
gnomAD - Exomes African Sub 16256 G=1.00000 A=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10080 G=1.00000 A=0.00000
gnomAD - Exomes Other Sub 6140 G=1.0000 A=0.0000
gnomAD - Genomes Global Study-wide 140196 G=1.000000 A=0.000000
gnomAD - Genomes European Sub 75930 G=1.00000 A=0.00000
gnomAD - Genomes African Sub 42014 G=1.00000 A=0.00000
gnomAD - Genomes American Sub 13646 G=1.00000 A=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3132 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2150 G=1.0000 A=0.0000
ExAC Global Study-wide 121382 G=0.999901 A=0.000099
ExAC Europe Sub 73352 G=1.00000 A=0.00000
ExAC Asian Sub 25166 G=0.99952 A=0.00048
ExAC American Sub 11550 G=1.00000 A=0.00000
ExAC African Sub 10406 G=1.00000 A=0.00000
ExAC Other Sub 908 G=1.000 A=0.000
Allele Frequency Aggregator Total Global 10680 G=1.00000 A=0.00000, C=0.00000
Allele Frequency Aggregator European Sub 6962 G=1.0000 A=0.0000, C=0.0000
Allele Frequency Aggregator African Sub 2294 G=1.0000 A=0.0000, C=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 G=1.000 A=0.000, C=0.000
Allele Frequency Aggregator Other Sub 466 G=1.000 A=0.000, C=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 G=1.000 A=0.000, C=0.000
Allele Frequency Aggregator Asian Sub 108 G=1.000 A=0.000, C=0.000
Allele Frequency Aggregator South Asian Sub 94 G=1.00 A=0.00, C=0.00
1000Genomes_30x Global Study-wide 6404 G=0.9998 A=0.0002
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=0.9992 A=0.0008
1000Genomes_30x East Asian Sub 1170 G=1.0000 A=0.0000
1000Genomes_30x American Sub 980 G=1.000 A=0.000
1000Genomes Global Study-wide 5008 G=0.9998 A=0.0002
1000Genomes African Sub 1322 G=1.0000 A=0.0000
1000Genomes East Asian Sub 1008 G=1.0000 A=0.0000
1000Genomes Europe Sub 1006 G=1.0000 A=0.0000
1000Genomes South Asian Sub 978 G=0.999 A=0.001
1000Genomes American Sub 694 G=1.000 A=0.000
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=1.0000 C=0.0000
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.9997 C=0.0003
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.132331819G>A
GRCh38.p14 chr 5 NC_000005.10:g.132331819G>C
GRCh37.p13 chr 5 NC_000005.9:g.131667512G>A
GRCh37.p13 chr 5 NC_000005.9:g.131667512G>C
SLC22A4 RefSeqGene NG_012129.2:g.42368G>A
SLC22A4 RefSeqGene NG_012129.2:g.42368G>C
Gene: SLC22A4, solute carrier family 22 member 4 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
SLC22A4 transcript NM_003059.3:c.1015G>A A [GCC] > T [ACC] Coding Sequence Variant
solute carrier family 22 member 4 NP_003050.2:p.Ala339Thr A (Ala) > T (Thr) Missense Variant
SLC22A4 transcript NM_003059.3:c.1015G>C A [GCC] > P [CCC] Coding Sequence Variant
solute carrier family 22 member 4 NP_003050.2:p.Ala339Pro A (Ala) > P (Pro) Missense Variant
SLC22A4 transcript variant X1 XM_047417594.1:c.1015G>A A [GCC] > T [ACC] Coding Sequence Variant
solute carrier family 22 member 4 isoform X1 XP_047273550.1:p.Ala339Thr A (Ala) > T (Thr) Missense Variant
SLC22A4 transcript variant X1 XM_047417594.1:c.1015G>C A [GCC] > P [CCC] Coding Sequence Variant
solute carrier family 22 member 4 isoform X1 XP_047273550.1:p.Ala339Pro A (Ala) > P (Pro) Missense Variant
SLC22A4 transcript variant X2 XM_011543589.3:c.739G>A A [GCC] > T [ACC] Coding Sequence Variant
solute carrier family 22 member 4 isoform X2 XP_011541891.1:p.Ala247Thr A (Ala) > T (Thr) Missense Variant
SLC22A4 transcript variant X2 XM_011543589.3:c.739G>C A [GCC] > P [CCC] Coding Sequence Variant
solute carrier family 22 member 4 isoform X2 XP_011541891.1:p.Ala247Pro A (Ala) > P (Pro) Missense Variant
SLC22A4 transcript variant X3 XM_017009776.2:c.487G>A A [GCC] > T [ACC] Coding Sequence Variant
solute carrier family 22 member 4 isoform X3 XP_016865265.1:p.Ala163Thr A (Ala) > T (Thr) Missense Variant
SLC22A4 transcript variant X3 XM_017009776.2:c.487G>C A [GCC] > P [CCC] Coding Sequence Variant
solute carrier family 22 member 4 isoform X3 XP_016865265.1:p.Ala163Pro A (Ala) > P (Pro) Missense Variant
SLC22A4 transcript variant X4 XM_006714675.5:c.487G>A A [GCC] > T [ACC] Coding Sequence Variant
solute carrier family 22 member 4 isoform X3 XP_006714738.1:p.Ala163Thr A (Ala) > T (Thr) Missense Variant
SLC22A4 transcript variant X4 XM_006714675.5:c.487G>C A [GCC] > P [CCC] Coding Sequence Variant
solute carrier family 22 member 4 isoform X3 XP_006714738.1:p.Ala163Pro A (Ala) > P (Pro) Missense Variant
Gene: MIR3936HG, MIR3936 host gene (minus strand)
Molecule type Change Amino acid[Codon] SO Term
MIR3936HG transcript NR_110997.1:n. 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 G= A C
GRCh38.p14 chr 5 NC_000005.10:g.132331819= NC_000005.10:g.132331819G>A NC_000005.10:g.132331819G>C
GRCh37.p13 chr 5 NC_000005.9:g.131667512= NC_000005.9:g.131667512G>A NC_000005.9:g.131667512G>C
SLC22A4 RefSeqGene NG_012129.2:g.42368= NG_012129.2:g.42368G>A NG_012129.2:g.42368G>C
SLC22A4 transcript NM_003059.3:c.1015= NM_003059.3:c.1015G>A NM_003059.3:c.1015G>C
SLC22A4 transcript NM_003059.2:c.1015= NM_003059.2:c.1015G>A NM_003059.2:c.1015G>C
SLC22A4 transcript variant X4 XM_006714675.5:c.487= XM_006714675.5:c.487G>A XM_006714675.5:c.487G>C
SLC22A4 transcript variant X3 XM_006714675.4:c.487= XM_006714675.4:c.487G>A XM_006714675.4:c.487G>C
SLC22A4 transcript variant X3 XM_006714675.3:c.487= XM_006714675.3:c.487G>A XM_006714675.3:c.487G>C
SLC22A4 transcript variant X2 XM_006714675.2:c.487= XM_006714675.2:c.487G>A XM_006714675.2:c.487G>C
SLC22A4 transcript variant X1 XM_006714675.1:c.487= XM_006714675.1:c.487G>A XM_006714675.1:c.487G>C
SLC22A4 transcript variant X2 XM_011543589.3:c.739= XM_011543589.3:c.739G>A XM_011543589.3:c.739G>C
SLC22A4 transcript variant X1 XM_011543589.2:c.739= XM_011543589.2:c.739G>A XM_011543589.2:c.739G>C
SLC22A4 transcript variant X1 XM_011543589.1:c.739= XM_011543589.1:c.739G>A XM_011543589.1:c.739G>C
SLC22A4 transcript variant X3 XM_017009776.2:c.487= XM_017009776.2:c.487G>A XM_017009776.2:c.487G>C
SLC22A4 transcript variant X2 XM_017009776.1:c.487= XM_017009776.1:c.487G>A XM_017009776.1:c.487G>C
SLC22A4 transcript variant X1 XM_047417594.1:c.1015= XM_047417594.1:c.1015G>A XM_047417594.1:c.1015G>C
solute carrier family 22 member 4 NP_003050.2:p.Ala339= NP_003050.2:p.Ala339Thr NP_003050.2:p.Ala339Pro
solute carrier family 22 member 4 isoform X3 XP_006714738.1:p.Ala163= XP_006714738.1:p.Ala163Thr XP_006714738.1:p.Ala163Pro
solute carrier family 22 member 4 isoform X2 XP_011541891.1:p.Ala247= XP_011541891.1:p.Ala247Thr XP_011541891.1:p.Ala247Pro
solute carrier family 22 member 4 isoform X3 XP_016865265.1:p.Ala163= XP_016865265.1:p.Ala163Thr XP_016865265.1:p.Ala163Pro
solute carrier family 22 member 4 isoform X1 XP_047273550.1:p.Ala339= XP_047273550.1:p.Ala339Thr XP_047273550.1:p.Ala339Pro
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#.

10 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss1317247085 Aug 21, 2014 (142)
2 EVA_UK10K_ALSPAC ss1614026719 Apr 01, 2015 (144)
3 EVA_UK10K_TWINSUK ss1657020752 Apr 01, 2015 (144)
4 EVA_EXAC ss1687940642 Apr 01, 2015 (144)
5 GNOMAD ss2735206920 Nov 08, 2017 (151)
6 GNOMAD ss4129447542 Apr 26, 2021 (155)
7 TOPMED ss4678964622 Apr 26, 2021 (155)
8 EVA ss5361009041 Oct 13, 2022 (156)
9 1000G_HIGH_COVERAGE ss5550532133 Oct 13, 2022 (156)
10 EVA ss5896351004 Oct 13, 2022 (156)
11 1000Genomes NC_000005.9 - 131667512 Oct 12, 2018 (152)
12 1000Genomes_30x NC_000005.10 - 132331819 Oct 13, 2022 (156)
13 The Avon Longitudinal Study of Parents and Children NC_000005.9 - 131667512 Oct 12, 2018 (152)
14 ExAC NC_000005.9 - 131667512 Oct 12, 2018 (152)
15 gnomAD - Genomes NC_000005.10 - 132331819 Apr 26, 2021 (155)
16 gnomAD - Exomes NC_000005.9 - 131667512 Jul 13, 2019 (153)
17 TopMed NC_000005.10 - 132331819 Apr 26, 2021 (155)
18 UK 10K study - Twins NC_000005.9 - 131667512 Oct 12, 2018 (152)
19 ALFA NC_000005.10 - 132331819 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
28926796, 7943043, 4330204, ss1317247085, ss1687940642, ss2735206920, ss5361009041 NC_000005.9:131667511:G:A NC_000005.10:132331818:G:A (self)
38058068, 204582568, 6940577203, ss4129447542, ss5550532133, ss5896351004 NC_000005.10:132331818:G:A NC_000005.10:132331818:G:A (self)
16087802, 16087802, ss1614026719, ss1657020752 NC_000005.9:131667511:G:C NC_000005.10:132331818:G:C (self)
516342179, 6940577203, ss4678964622 NC_000005.10:132331818:G:C NC_000005.10:132331818:G: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 rs533127429

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