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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.

rs28639892

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr4:71189668 (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>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.007450 (1972/264690, TOPMED)
G=0.006614 (928/140300, GnomAD)
G=0.00870 (167/19190, ALFA) (+ 12 more)
G=0.0042 (27/6404, 1000G_30x)
G=0.0046 (23/5008, 1000G)
G=0.0067 (30/4480, Estonian)
G=0.0080 (31/3854, ALSPAC)
G=0.0076 (28/3708, TWINSUK)
G=0.004 (4/998, GoNL)
G=0.003 (2/600, NorthernSweden)
G=0.028 (6/216, Qatari)
A=0.5 (3/6, SGDP_PRJ)
G=0.5 (3/6, SGDP_PRJ)
A=0.5 (1/2, Siberian)
G=0.5 (1/2, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SLC4A4 : 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 19190 A=0.99130 G=0.00870
European Sub 14286 A=0.98957 G=0.01043
African Sub 2970 A=0.9987 G=0.0013
African Others Sub 114 A=1.000 G=0.000
African American Sub 2856 A=0.9986 G=0.0014
Asian Sub 116 A=1.000 G=0.000
East Asian Sub 88 A=1.00 G=0.00
Other Asian Sub 28 A=1.00 G=0.00
Latin American 1 Sub 154 A=0.981 G=0.019
Latin American 2 Sub 616 A=0.995 G=0.005
South Asian Sub 98 A=0.99 G=0.01
Other Sub 950 A=0.993 G=0.007


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=0.992550 G=0.007450
gnomAD - Genomes Global Study-wide 140300 A=0.993386 G=0.006614
gnomAD - Genomes European Sub 75966 A=0.99173 G=0.00827
gnomAD - Genomes African Sub 42064 A=0.99826 G=0.00174
gnomAD - Genomes American Sub 13664 A=0.99224 G=0.00776
gnomAD - Genomes Ashkenazi Jewish Sub 3320 A=0.9693 G=0.0307
gnomAD - Genomes East Asian Sub 3132 A=1.0000 G=0.0000
gnomAD - Genomes Other Sub 2154 A=0.9912 G=0.0088
Allele Frequency Aggregator Total Global 19190 A=0.99130 G=0.00870
Allele Frequency Aggregator European Sub 14286 A=0.98957 G=0.01043
Allele Frequency Aggregator African Sub 2970 A=0.9987 G=0.0013
Allele Frequency Aggregator Other Sub 950 A=0.993 G=0.007
Allele Frequency Aggregator Latin American 2 Sub 616 A=0.995 G=0.005
Allele Frequency Aggregator Latin American 1 Sub 154 A=0.981 G=0.019
Allele Frequency Aggregator Asian Sub 116 A=1.000 G=0.000
Allele Frequency Aggregator South Asian Sub 98 A=0.99 G=0.01
1000Genomes_30x Global Study-wide 6404 A=0.9958 G=0.0042
1000Genomes_30x African Sub 1786 A=1.0000 G=0.0000
1000Genomes_30x Europe Sub 1266 A=0.9953 G=0.0047
1000Genomes_30x South Asian Sub 1202 A=0.9925 G=0.0075
1000Genomes_30x East Asian Sub 1170 A=1.0000 G=0.0000
1000Genomes_30x American Sub 980 A=0.988 G=0.012
1000Genomes Global Study-wide 5008 A=0.9954 G=0.0046
1000Genomes African Sub 1322 A=1.0000 G=0.0000
1000Genomes East Asian Sub 1008 A=1.0000 G=0.0000
1000Genomes Europe Sub 1006 A=0.9950 G=0.0050
1000Genomes South Asian Sub 978 A=0.992 G=0.008
1000Genomes American Sub 694 A=0.986 G=0.014
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.9933 G=0.0067
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.9920 G=0.0080
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.9924 G=0.0076
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.996 G=0.004
Northern Sweden ACPOP Study-wide 600 A=0.997 G=0.003
Qatari Global Study-wide 216 A=0.972 G=0.028
SGDP_PRJ Global Study-wide 6 A=0.5 G=0.5
Siberian Global Study-wide 2 A=0.5 G=0.5
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 4 NC_000004.12:g.71189668A>G
GRCh37.p13 chr 4 NC_000004.11:g.72055385A>G
SLC4A4 RefSeqGene NG_012653.1:g.7383A>G
Gene: SLC4A4, solute carrier family 4 member 4 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
SLC4A4 transcript variant 1 NM_001098484.3:c.-2+2267A…

NM_001098484.3:c.-2+2267A>G

N/A Intron Variant
SLC4A4 transcript variant 3 NM_001134742.2:c.-2+2267A…

NM_001134742.2:c.-2+2267A>G

N/A Intron Variant
SLC4A4 transcript variant 2 NM_003759.4:c. N/A Genic Upstream Transcript Variant
SLC4A4 transcript variant X3 XM_024454268.2:c.15-46908…

XM_024454268.2:c.15-46908A>G

N/A Intron Variant
SLC4A4 transcript variant X2 XM_024454269.2:c.15-46908…

XM_024454269.2:c.15-46908A>G

N/A Intron Variant
SLC4A4 transcript variant X9 XM_011532390.3:c. N/A Genic Upstream Transcript Variant
SLC4A4 transcript variant X7 XM_017008792.2:c. N/A Genic Upstream Transcript Variant
SLC4A4 transcript variant X8 XM_017008793.2:c. N/A Genic Upstream Transcript Variant
SLC4A4 transcript variant X1 XM_024454267.2:c. N/A Genic Upstream Transcript Variant
SLC4A4 transcript variant X5 XM_024454270.2:c. N/A Genic Upstream Transcript Variant
SLC4A4 transcript variant X6 XM_024454271.2:c. N/A Genic Upstream Transcript Variant
SLC4A4 transcript variant X4 XM_024454272.2:c. N/A Genic Upstream Transcript Variant
SLC4A4 transcript variant X10 XM_047416348.1:c. N/A Genic Upstream Transcript 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= G
GRCh38.p14 chr 4 NC_000004.12:g.71189668= NC_000004.12:g.71189668A>G
GRCh37.p13 chr 4 NC_000004.11:g.72055385= NC_000004.11:g.72055385A>G
SLC4A4 RefSeqGene NG_012653.1:g.7383= NG_012653.1:g.7383A>G
SLC4A4 transcript variant 1 NM_001098484.2:c.-2+2267= NM_001098484.2:c.-2+2267A>G
SLC4A4 transcript variant 1 NM_001098484.3:c.-2+2267= NM_001098484.3:c.-2+2267A>G
SLC4A4 transcript variant 3 NM_001134742.1:c.-2+2267= NM_001134742.1:c.-2+2267A>G
SLC4A4 transcript variant 3 NM_001134742.2:c.-2+2267= NM_001134742.2:c.-2+2267A>G
SLC4A4 transcript variant X3 XM_005265705.1:c.-2+2267= XM_005265705.1:c.-2+2267A>G
SLC4A4 transcript variant X3 XM_024454268.2:c.15-46908= XM_024454268.2:c.15-46908A>G
SLC4A4 transcript variant X2 XM_024454269.2:c.15-46908= XM_024454269.2:c.15-46908A>G
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#.

31 SubSNP, 13 Frequency submissions
No Submitter Submission ID Date (Build)
1 SSAHASNP ss35394123 May 24, 2005 (125)
2 1000GENOMES ss331715330 May 09, 2011 (134)
3 ILLUMINA ss535969305 Sep 08, 2015 (146)
4 TISHKOFF ss557588851 Apr 25, 2013 (138)
5 EVA-GONL ss980236897 Aug 21, 2014 (142)
6 1000GENOMES ss1310198449 Aug 21, 2014 (142)
7 DDI ss1429920224 Apr 01, 2015 (144)
8 EVA_DECODE ss1589736309 Apr 01, 2015 (144)
9 EVA_UK10K_ALSPAC ss1610316706 Apr 01, 2015 (144)
10 EVA_UK10K_TWINSUK ss1653310739 Apr 01, 2015 (144)
11 WEILL_CORNELL_DGM ss1923480037 Feb 12, 2016 (147)
12 JJLAB ss2022326259 Sep 14, 2016 (149)
13 USC_VALOUEV ss2150453659 Dec 20, 2016 (150)
14 HUMAN_LONGEVITY ss2263779007 Dec 20, 2016 (150)
15 GNOMAD ss2810609894 Nov 08, 2017 (151)
16 SWEGEN ss2994890503 Nov 08, 2017 (151)
17 ILLUMINA ss3628986748 Oct 12, 2018 (152)
18 EGCUT_WGS ss3662772066 Jul 13, 2019 (153)
19 EVA_DECODE ss3712274282 Jul 13, 2019 (153)
20 ACPOP ss3731252708 Jul 13, 2019 (153)
21 EVA ss3761936673 Jul 13, 2019 (153)
22 SGDP_PRJ ss3859198983 Apr 26, 2020 (154)
23 TOPMED ss4617754051 Apr 26, 2021 (155)
24 1000G_HIGH_COVERAGE ss5259605019 Oct 17, 2022 (156)
25 EVA ss5349732862 Oct 17, 2022 (156)
26 HUGCELL_USP ss5458321081 Oct 17, 2022 (156)
27 1000G_HIGH_COVERAGE ss5540906204 Oct 17, 2022 (156)
28 SANFORD_IMAGENETICS ss5635271645 Oct 17, 2022 (156)
29 EVA ss5844154690 Oct 17, 2022 (156)
30 EVA ss5863895317 Oct 17, 2022 (156)
31 EVA ss5963645264 Oct 17, 2022 (156)
32 1000Genomes NC_000004.11 - 72055385 Oct 12, 2018 (152)
33 1000Genomes_30x NC_000004.12 - 71189668 Oct 17, 2022 (156)
34 The Avon Longitudinal Study of Parents and Children NC_000004.11 - 72055385 Oct 12, 2018 (152)
35 Genetic variation in the Estonian population NC_000004.11 - 72055385 Oct 12, 2018 (152)
36 gnomAD - Genomes NC_000004.12 - 71189668 Apr 26, 2021 (155)
37 Genome of the Netherlands Release 5 NC_000004.11 - 72055385 Apr 26, 2020 (154)
38 Northern Sweden NC_000004.11 - 72055385 Jul 13, 2019 (153)
39 Qatari NC_000004.11 - 72055385 Apr 26, 2020 (154)
40 SGDP_PRJ NC_000004.11 - 72055385 Apr 26, 2020 (154)
41 Siberian NC_000004.11 - 72055385 Apr 26, 2020 (154)
42 TopMed NC_000004.12 - 71189668 Apr 26, 2021 (155)
43 UK 10K study - Twins NC_000004.11 - 72055385 Oct 12, 2018 (152)
44 ALFA NC_000004.12 - 71189668 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
ss35394123 NC_000004.9:72420419:A:G NC_000004.12:71189667:A:G (self)
ss1589736309 NC_000004.10:72274248:A:G NC_000004.12:71189667:A:G (self)
21610375, 12012142, 8510314, 5305422, 4537573, 5521967, 11215963, 2970013, 12012142, ss331715330, ss535969305, ss557588851, ss980236897, ss1310198449, ss1429920224, ss1610316706, ss1653310739, ss1923480037, ss2022326259, ss2150453659, ss2810609894, ss2994890503, ss3628986748, ss3662772066, ss3731252708, ss3761936673, ss3859198983, ss5349732862, ss5635271645, ss5844154690, ss5963645264 NC_000004.11:72055384:A:G NC_000004.12:71189667:A:G (self)
28432139, 153089395, 455131607, 14090110625, ss2263779007, ss3712274282, ss4617754051, ss5259605019, ss5458321081, ss5540906204, ss5863895317 NC_000004.12:71189667:A:G NC_000004.12:71189667:A:G (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 rs28639892

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