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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.

rs79308473

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr14:70046810 (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=0.000029 (4/140212, GnomAD)
A=0.00237 (67/28258, 14KJPN)
A=0.00215 (36/16760, 8.3KJPN) (+ 7 more)
A=0.00000 (0/14050, ALFA)
C=0.00000 (0/14050, ALFA)
A=0.0002 (1/6404, 1000G_30x)
A=0.0002 (1/5008, 1000G)
C=0.0005 (2/3854, ALSPAC)
C=0.0000 (0/3708, TWINSUK)
A=0.0003 (1/2922, KOREAN)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SLC8A3 : 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 14050 G=1.00000 A=0.00000, C=0.00000
European Sub 9690 G=1.0000 A=0.0000, C=0.0000
African Sub 2898 G=1.0000 A=0.0000, C=0.0000
African Others Sub 114 G=1.000 A=0.000, C=0.000
African American Sub 2784 G=1.0000 A=0.0000, C=0.0000
Asian Sub 112 G=1.000 A=0.000, C=0.000
East Asian Sub 86 G=1.00 A=0.00, C=0.00
Other Asian Sub 26 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 98 G=1.00 A=0.00, C=0.00
Other Sub 496 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
gnomAD - Genomes Global Study-wide 140212 G=0.999971 C=0.000029
gnomAD - Genomes European Sub 75934 G=0.99995 C=0.00005
gnomAD - Genomes African Sub 42016 G=1.00000 C=0.00000
gnomAD - Genomes American Sub 13656 G=1.00000 C=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=1.0000 C=0.0000
gnomAD - Genomes East Asian Sub 3132 G=1.0000 C=0.0000
gnomAD - Genomes Other Sub 2150 G=1.0000 C=0.0000
14KJPN JAPANESE Study-wide 28258 G=0.99763 A=0.00237
8.3KJPN JAPANESE Study-wide 16760 G=0.99785 A=0.00215
Allele Frequency Aggregator Total Global 14050 G=1.00000 A=0.00000, C=0.00000
Allele Frequency Aggregator European Sub 9690 G=1.0000 A=0.0000, C=0.0000
Allele Frequency Aggregator African Sub 2898 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 496 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 112 G=1.000 A=0.000, C=0.000
Allele Frequency Aggregator South Asian Sub 98 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=1.0000 A=0.0000
1000Genomes_30x East Asian Sub 1170 G=0.9991 A=0.0009
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=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=1.000 A=0.000
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.9995 C=0.0005
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=1.0000 C=0.0000
KOREAN population from KRGDB KOREAN Study-wide 2922 G=0.9997 A=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 14 NC_000014.9:g.70046810G>A
GRCh38.p14 chr 14 NC_000014.9:g.70046810G>C
GRCh37.p13 chr 14 NC_000014.8:g.70513527G>A
GRCh37.p13 chr 14 NC_000014.8:g.70513527G>C
SLC8A3 RefSeqGene NG_047080.1:g.181803C>T
SLC8A3 RefSeqGene NG_047080.1:g.181803C>G
Gene: SLC8A3, solute carrier family 8 member A3 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
SLC8A3 transcript variant g NM_001130417.3:c.521-487C…

NM_001130417.3:c.521-487C>T

N/A Intron Variant
SLC8A3 transcript variant a NM_033262.5:c.2402-487C>T N/A Intron Variant
SLC8A3 transcript variant b NM_058240.4:c.2399-487C>T N/A Intron Variant
SLC8A3 transcript variant d NM_182932.3:c.2390-487C>T N/A Intron Variant
SLC8A3 transcript variant f NM_182936.3:c.479-487C>T N/A Intron Variant
SLC8A3 transcript variant c NM_183002.3:c.2408-487C>T N/A Intron Variant
SLC8A3 transcript variant h NR_104122.2:n. N/A Intron Variant
SLC8A3 transcript variant X8 XM_006720240.4:c.539-487C…

XM_006720240.4:c.539-487C>T

N/A Intron Variant
SLC8A3 transcript variant X1 XM_017021606.2:c.2408-487…

XM_017021606.2:c.2408-487C>T

N/A Intron Variant
SLC8A3 transcript variant X2 XM_017021607.2:c.2405-487…

XM_017021607.2:c.2405-487C>T

N/A Intron Variant
SLC8A3 transcript variant X3 XM_017021608.2:c.2390-487…

XM_017021608.2:c.2390-487C>T

N/A Intron Variant
SLC8A3 transcript variant X4 XM_017021609.2:c.2387-487…

XM_017021609.2:c.2387-487C>T

N/A Intron Variant
SLC8A3 transcript variant X7 XM_017021611.2:c.560-487C…

XM_017021611.2:c.560-487C>T

N/A Intron Variant
SLC8A3 transcript variant X5 XM_047431711.1:c.2387-487…

XM_047431711.1:c.2387-487C>T

N/A Intron Variant
SLC8A3 transcript variant X6 XM_017021610.2:c. N/A Genic Downstream 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 G= A C
GRCh38.p14 chr 14 NC_000014.9:g.70046810= NC_000014.9:g.70046810G>A NC_000014.9:g.70046810G>C
GRCh37.p13 chr 14 NC_000014.8:g.70513527= NC_000014.8:g.70513527G>A NC_000014.8:g.70513527G>C
SLC8A3 RefSeqGene NG_047080.1:g.181803= NG_047080.1:g.181803C>T NG_047080.1:g.181803C>G
SLC8A3 transcript variant g NM_001130417.1:c.521-487= NM_001130417.1:c.521-487C>T NM_001130417.1:c.521-487C>G
SLC8A3 transcript variant g NM_001130417.3:c.521-487= NM_001130417.3:c.521-487C>T NM_001130417.3:c.521-487C>G
SLC8A3 transcript variant a NM_033262.3:c.2402-487= NM_033262.3:c.2402-487C>T NM_033262.3:c.2402-487C>G
SLC8A3 transcript variant a NM_033262.5:c.2402-487= NM_033262.5:c.2402-487C>T NM_033262.5:c.2402-487C>G
SLC8A3 transcript variant b NM_058240.2:c.2399-487= NM_058240.2:c.2399-487C>T NM_058240.2:c.2399-487C>G
SLC8A3 transcript variant b NM_058240.4:c.2399-487= NM_058240.4:c.2399-487C>T NM_058240.4:c.2399-487C>G
SLC8A3 transcript variant d NM_182932.1:c.2390-487= NM_182932.1:c.2390-487C>T NM_182932.1:c.2390-487C>G
SLC8A3 transcript variant d NM_182932.3:c.2390-487= NM_182932.3:c.2390-487C>T NM_182932.3:c.2390-487C>G
SLC8A3 transcript variant f NM_182936.1:c.479-487= NM_182936.1:c.479-487C>T NM_182936.1:c.479-487C>G
SLC8A3 transcript variant f NM_182936.3:c.479-487= NM_182936.3:c.479-487C>T NM_182936.3:c.479-487C>G
SLC8A3 transcript variant c NM_183002.1:c.2408-487= NM_183002.1:c.2408-487C>T NM_183002.1:c.2408-487C>G
SLC8A3 transcript variant c NM_183002.3:c.2408-487= NM_183002.3:c.2408-487C>T NM_183002.3:c.2408-487C>G
SLC8A3 transcript variant X1 XM_005268017.1:c.2411-487= XM_005268017.1:c.2411-487C>T XM_005268017.1:c.2411-487C>G
SLC8A3 transcript variant X2 XM_005268018.1:c.2009-487= XM_005268018.1:c.2009-487C>T XM_005268018.1:c.2009-487C>G
SLC8A3 transcript variant X8 XM_006720240.4:c.539-487= XM_006720240.4:c.539-487C>T XM_006720240.4:c.539-487C>G
SLC8A3 transcript variant X1 XM_017021606.2:c.2408-487= XM_017021606.2:c.2408-487C>T XM_017021606.2:c.2408-487C>G
SLC8A3 transcript variant X2 XM_017021607.2:c.2405-487= XM_017021607.2:c.2405-487C>T XM_017021607.2:c.2405-487C>G
SLC8A3 transcript variant X3 XM_017021608.2:c.2390-487= XM_017021608.2:c.2390-487C>T XM_017021608.2:c.2390-487C>G
SLC8A3 transcript variant X4 XM_017021609.2:c.2387-487= XM_017021609.2:c.2387-487C>T XM_017021609.2:c.2387-487C>G
SLC8A3 transcript variant X7 XM_017021611.2:c.560-487= XM_017021611.2:c.560-487C>T XM_017021611.2:c.560-487C>G
SLC8A3 transcript variant X5 XM_047431711.1:c.2387-487= XM_047431711.1:c.2387-487C>T XM_047431711.1:c.2387-487C>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#.

16 SubSNP, 11 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss243015010 Jul 15, 2010 (132)
2 1000GENOMES ss1351512311 Aug 21, 2014 (142)
3 EVA_UK10K_ALSPAC ss1632009429 Apr 01, 2015 (144)
4 EVA_UK10K_TWINSUK ss1675003462 Apr 01, 2015 (144)
5 HUMAN_LONGEVITY ss2203040012 Dec 20, 2016 (150)
6 EVA ss3752478090 Jul 13, 2019 (153)
7 KRGDB ss3930816250 Apr 27, 2020 (154)
8 GNOMAD ss4280250475 Apr 26, 2021 (155)
9 TOPMED ss4975074205 Apr 26, 2021 (155)
10 TOPMED ss4975074206 Apr 26, 2021 (155)
11 TOMMO_GENOMICS ss5213805603 Apr 26, 2021 (155)
12 EVA ss5416072962 Oct 16, 2022 (156)
13 1000G_HIGH_COVERAGE ss5597173859 Oct 16, 2022 (156)
14 TOMMO_GENOMICS ss5766774371 Oct 16, 2022 (156)
15 EVA ss5901853295 Oct 16, 2022 (156)
16 EVA ss5947917943 Oct 16, 2022 (156)
17 1000Genomes NC_000014.8 - 70513527 Oct 12, 2018 (152)
18 1000Genomes_30x NC_000014.9 - 70046810 Oct 16, 2022 (156)
19 The Avon Longitudinal Study of Parents and Children NC_000014.8 - 70513527 Oct 12, 2018 (152)
20 gnomAD - Genomes NC_000014.9 - 70046810 Apr 26, 2021 (155)
21 KOREAN population from KRGDB NC_000014.8 - 70513527 Apr 27, 2020 (154)
22 8.3KJPN NC_000014.8 - 70513527 Apr 26, 2021 (155)
23 14KJPN NC_000014.9 - 70046810 Oct 16, 2022 (156)
24 TopMed

Submission ignored due to conflicting rows:
Row 190619864 (NC_000014.9:70046809:G:A 1/264690)
Row 190619865 (NC_000014.9:70046809:G:C 9/264690)

- Apr 26, 2021 (155)
25 TopMed

Submission ignored due to conflicting rows:
Row 190619864 (NC_000014.9:70046809:G:A 1/264690)
Row 190619865 (NC_000014.9:70046809:G:C 9/264690)

- Apr 26, 2021 (155)
26 UK 10K study - Twins NC_000014.8 - 70513527 Oct 12, 2018 (152)
27 ALFA NC_000014.9 - 70046810 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
64512319, 37993644, 71774910, ss243015010, ss1351512311, ss3752478090, ss3930816250, ss5213805603, ss5416072962 NC_000014.8:70513526:G:A NC_000014.9:70046809:G:A (self)
84699794, 100611475, 1318402795, ss4975074205, ss5597173859, ss5766774371, ss5901853295 NC_000014.9:70046809:G:A NC_000014.9:70046809:G:A (self)
35845475, 35845475, ss1632009429, ss1675003462, ss5947917943 NC_000014.8:70513526:G:C NC_000014.9:70046809:G:C (self)
454867374, 1318402795, ss2203040012, ss4280250475, ss4975074206 NC_000014.9:70046809:G:C NC_000014.9:70046809: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 rs79308473

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