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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.

rs78725444

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr14:36989079 (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=0.003593 (951/264690, TOPMED)
A=0.005634 (790/140224, GnomAD)
A=0.00021 (6/28258, 14KJPN) (+ 12 more)
A=0.00604 (116/19190, ALFA)
A=0.00024 (4/16760, 8.3KJPN)
A=0.0023 (15/6404, 1000G_30x)
A=0.0020 (10/5008, 1000G)
A=0.0094 (42/4480, Estonian)
A=0.0083 (32/3854, ALSPAC)
A=0.0067 (25/3708, TWINSUK)
A=0.007 (7/998, GoNL)
A=0.015 (9/600, NorthernSweden)
A=0.005 (1/216, Qatari)
G=0.50 (7/14, SGDP_PRJ)
A=0.50 (7/14, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SLC25A21 : 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 G=0.99396 A=0.00604
European Sub 14286 G=0.99251 A=0.00749
African Sub 2970 G=0.9993 A=0.0007
African Others Sub 114 G=1.000 A=0.000
African American Sub 2856 G=0.9993 A=0.0007
Asian Sub 116 G=1.000 A=0.000
East Asian Sub 88 G=1.00 A=0.00
Other Asian Sub 28 G=1.00 A=0.00
Latin American 1 Sub 154 G=0.994 A=0.006
Latin American 2 Sub 616 G=0.995 A=0.005
South Asian Sub 98 G=1.00 A=0.00
Other Sub 950 G=0.997 A=0.003


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=0.996407 A=0.003593
gnomAD - Genomes Global Study-wide 140224 G=0.994366 A=0.005634
gnomAD - Genomes European Sub 75932 G=0.99089 A=0.00911
gnomAD - Genomes African Sub 42022 G=0.99843 A=0.00157
gnomAD - Genomes American Sub 13662 G=0.99817 A=0.00183
gnomAD - Genomes Ashkenazi Jewish Sub 3322 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3134 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2152 G=0.9967 A=0.0033
14KJPN JAPANESE Study-wide 28258 G=0.99979 A=0.00021
Allele Frequency Aggregator Total Global 19190 G=0.99396 A=0.00604
Allele Frequency Aggregator European Sub 14286 G=0.99251 A=0.00749
Allele Frequency Aggregator African Sub 2970 G=0.9993 A=0.0007
Allele Frequency Aggregator Other Sub 950 G=0.997 A=0.003
Allele Frequency Aggregator Latin American 2 Sub 616 G=0.995 A=0.005
Allele Frequency Aggregator Latin American 1 Sub 154 G=0.994 A=0.006
Allele Frequency Aggregator Asian Sub 116 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 98 G=1.00 A=0.00
8.3KJPN JAPANESE Study-wide 16760 G=0.99976 A=0.00024
1000Genomes_30x Global Study-wide 6404 G=0.9977 A=0.0023
1000Genomes_30x African Sub 1786 G=0.9983 A=0.0017
1000Genomes_30x Europe Sub 1266 G=0.9921 A=0.0079
1000Genomes_30x South Asian Sub 1202 G=1.0000 A=0.0000
1000Genomes_30x East Asian Sub 1170 G=1.0000 A=0.0000
1000Genomes_30x American Sub 980 G=0.998 A=0.002
1000Genomes Global Study-wide 5008 G=0.9980 A=0.0020
1000Genomes African Sub 1322 G=0.9985 A=0.0015
1000Genomes East Asian Sub 1008 G=1.0000 A=0.0000
1000Genomes Europe Sub 1006 G=0.9930 A=0.0070
1000Genomes South Asian Sub 978 G=1.000 A=0.000
1000Genomes American Sub 694 G=0.999 A=0.001
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.9906 A=0.0094
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.9917 A=0.0083
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.9933 A=0.0067
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.993 A=0.007
Northern Sweden ACPOP Study-wide 600 G=0.985 A=0.015
Qatari Global Study-wide 216 G=0.995 A=0.005
SGDP_PRJ Global Study-wide 14 G=0.50 A=0.50
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.36989079G>A
GRCh37.p13 chr 14 NC_000014.8:g.37458284G>A
Gene: SLC25A21, solute carrier family 25 member 21 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
SLC25A21 transcript variant 2 NM_001171170.2:c.71-11407…

NM_001171170.2:c.71-114075C>T

N/A Intron Variant
SLC25A21 transcript variant 1 NM_030631.4:c.71-114075C>T N/A Intron Variant
SLC25A21 transcript variant X1 XM_047431871.1:c.71-11407…

XM_047431871.1:c.71-114075C>T

N/A Intron Variant
SLC25A21 transcript variant X2 XM_011537288.4:c. N/A Genic Upstream Transcript Variant
SLC25A21 transcript variant X3 XM_011537289.4: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 G= A
GRCh38.p14 chr 14 NC_000014.9:g.36989079= NC_000014.9:g.36989079G>A
GRCh37.p13 chr 14 NC_000014.8:g.37458284= NC_000014.8:g.37458284G>A
SLC25A21 transcript variant 2 NM_001171170.1:c.71-114075= NM_001171170.1:c.71-114075C>T
SLC25A21 transcript variant 2 NM_001171170.2:c.71-114075= NM_001171170.2:c.71-114075C>T
SLC25A21 transcript variant 1 NM_030631.3:c.71-114075= NM_030631.3:c.71-114075C>T
SLC25A21 transcript variant 1 NM_030631.4:c.71-114075= NM_030631.4:c.71-114075C>T
SLC25A21 transcript variant X1 XM_047431871.1:c.71-114075= XM_047431871.1:c.71-114075C>T
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#.

29 SubSNP, 14 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss236498889 Jul 15, 2010 (132)
2 ILLUMINA ss536086489 Sep 08, 2015 (146)
3 EVA-GONL ss991029566 Aug 21, 2014 (142)
4 1000GENOMES ss1350571781 Aug 21, 2014 (142)
5 EVA_UK10K_ALSPAC ss1631509867 Apr 01, 2015 (144)
6 EVA_UK10K_TWINSUK ss1674503900 Apr 01, 2015 (144)
7 EVA_DECODE ss1695024240 Apr 01, 2015 (144)
8 WEILL_CORNELL_DGM ss1934406324 Feb 12, 2016 (147)
9 JJLAB ss2027978535 Sep 14, 2016 (149)
10 HUMAN_LONGEVITY ss2201085965 Dec 20, 2016 (150)
11 GNOMAD ss2926460506 Nov 08, 2017 (151)
12 SWEGEN ss3012024874 Nov 08, 2017 (151)
13 ILLUMINA ss3627196834 Oct 12, 2018 (152)
14 EGCUT_WGS ss3679268171 Jul 13, 2019 (153)
15 EVA_DECODE ss3696467188 Jul 13, 2019 (153)
16 ACPOP ss3740285046 Jul 13, 2019 (153)
17 EVA ss3833861374 Apr 27, 2020 (154)
18 SGDP_PRJ ss3881275467 Apr 27, 2020 (154)
19 TOPMED ss4966877266 Apr 26, 2021 (155)
20 TOMMO_GENOMICS ss5212746132 Apr 26, 2021 (155)
21 1000G_HIGH_COVERAGE ss5295841446 Oct 16, 2022 (156)
22 EVA ss5414588379 Oct 16, 2022 (156)
23 HUGCELL_USP ss5489933665 Oct 16, 2022 (156)
24 1000G_HIGH_COVERAGE ss5595920163 Oct 16, 2022 (156)
25 SANFORD_IMAGENETICS ss5655999339 Oct 16, 2022 (156)
26 TOMMO_GENOMICS ss5765411455 Oct 16, 2022 (156)
27 EVA ss5840957485 Oct 16, 2022 (156)
28 EVA ss5900909867 Oct 16, 2022 (156)
29 EVA ss5947423710 Oct 16, 2022 (156)
30 1000Genomes NC_000014.8 - 37458284 Oct 12, 2018 (152)
31 1000Genomes_30x NC_000014.9 - 36989079 Oct 16, 2022 (156)
32 The Avon Longitudinal Study of Parents and Children NC_000014.8 - 37458284 Oct 12, 2018 (152)
33 Genetic variation in the Estonian population NC_000014.8 - 37458284 Oct 12, 2018 (152)
34 gnomAD - Genomes NC_000014.9 - 36989079 Apr 26, 2021 (155)
35 Genome of the Netherlands Release 5 NC_000014.8 - 37458284 Apr 27, 2020 (154)
36 Northern Sweden NC_000014.8 - 37458284 Jul 13, 2019 (153)
37 Qatari NC_000014.8 - 37458284 Apr 27, 2020 (154)
38 SGDP_PRJ NC_000014.8 - 37458284 Apr 27, 2020 (154)
39 8.3KJPN NC_000014.8 - 37458284 Apr 26, 2021 (155)
40 14KJPN NC_000014.9 - 36989079 Oct 16, 2022 (156)
41 TopMed NC_000014.9 - 36989079 Apr 26, 2021 (155)
42 UK 10K study - Twins NC_000014.8 - 37458284 Oct 12, 2018 (152)
43 ALFA NC_000014.9 - 36989079 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
ss1695024240 NC_000014.7:36528034:G:A NC_000014.9:36989078:G:A (self)
63535433, 35295317, 25006419, 15763835, 13569911, 16448254, 33292447, 70715439, 35295317, ss236498889, ss536086489, ss991029566, ss1350571781, ss1631509867, ss1674503900, ss1934406324, ss2027978535, ss2926460506, ss3012024874, ss3627196834, ss3679268171, ss3740285046, ss3833861374, ss3881275467, ss5212746132, ss5414588379, ss5655999339, ss5840957485, ss5947423710 NC_000014.8:37458283:G:A NC_000014.9:36989078:G:A (self)
83446098, 448030115, 99248559, 182422925, 159393904, ss2201085965, ss3696467188, ss4966877266, ss5295841446, ss5489933665, ss5595920163, ss5765411455, ss5900909867 NC_000014.9:36989078:G:A NC_000014.9:36989078: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 rs78725444

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