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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.

rs80021793

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr19:35119133 (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
T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.015989 (4232/264690, TOPMED)
C=0.014013 (2174/155140, GnomAD_exome)
C=0.014233 (1996/140236, GnomAD) (+ 17 more)
C=0.00011 (3/28258, 14KJPN)
C=0.01696 (478/28178, ALFA)
C=0.01361 (278/20422, ExAC)
C=0.00012 (2/16760, 8.3KJPN)
C=0.0095 (61/6404, 1000G_30x)
C=0.0094 (47/5008, 1000G)
C=0.0177 (81/4566, GO-ESP)
C=0.0054 (24/4480, Estonian)
C=0.0200 (77/3854, ALSPAC)
C=0.0186 (69/3708, TWINSUK)
C=0.015 (15/998, GoNL)
C=0.008 (5/600, NorthernSweden)
C=0.021 (11/534, MGP)
C=0.032 (7/216, Qatari)
C=0.03 (1/40, GENOME_DK)
T=0.50 (6/12, SGDP_PRJ)
C=0.50 (6/12, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
FXYD3 : 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 28178 T=0.98304 C=0.01696
European Sub 20348 T=0.98226 C=0.01774
African Sub 3564 T=0.9916 C=0.0084
African Others Sub 122 T=1.000 C=0.000
African American Sub 3442 T=0.9913 C=0.0087
Asian Sub 172 T=1.000 C=0.000
East Asian Sub 114 T=1.000 C=0.000
Other Asian Sub 58 T=1.00 C=0.00
Latin American 1 Sub 154 T=0.987 C=0.013
Latin American 2 Sub 616 T=0.984 C=0.016
South Asian Sub 98 T=0.99 C=0.01
Other Sub 3226 T=0.9771 C=0.0229


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 T=0.984011 C=0.015989
gnomAD - Exomes Global Study-wide 155140 T=0.985987 C=0.014013
gnomAD - Exomes European Sub 75264 T=0.98257 C=0.01743
gnomAD - Exomes Asian Sub 34194 T=0.99506 C=0.00494
gnomAD - Exomes American Sub 24764 T=0.98373 C=0.01627
gnomAD - Exomes Ashkenazi Jewish Sub 8496 T=0.9798 C=0.0202
gnomAD - Exomes African Sub 8064 T=0.9970 C=0.0030
gnomAD - Exomes Other Sub 4358 T=0.9784 C=0.0216
gnomAD - Genomes Global Study-wide 140236 T=0.985767 C=0.014233
gnomAD - Genomes European Sub 75926 T=0.98211 C=0.01789
gnomAD - Genomes African Sub 42038 T=0.99627 C=0.00373
gnomAD - Genomes American Sub 13664 T=0.97417 C=0.02583
gnomAD - Genomes Ashkenazi Jewish Sub 3324 T=0.9795 C=0.0205
gnomAD - Genomes East Asian Sub 3132 T=1.0000 C=0.0000
gnomAD - Genomes Other Sub 2152 T=0.9721 C=0.0279
14KJPN JAPANESE Study-wide 28258 T=0.99989 C=0.00011
Allele Frequency Aggregator Total Global 28178 T=0.98304 C=0.01696
Allele Frequency Aggregator European Sub 20348 T=0.98226 C=0.01774
Allele Frequency Aggregator African Sub 3564 T=0.9916 C=0.0084
Allele Frequency Aggregator Other Sub 3226 T=0.9771 C=0.0229
Allele Frequency Aggregator Latin American 2 Sub 616 T=0.984 C=0.016
Allele Frequency Aggregator Asian Sub 172 T=1.000 C=0.000
Allele Frequency Aggregator Latin American 1 Sub 154 T=0.987 C=0.013
Allele Frequency Aggregator South Asian Sub 98 T=0.99 C=0.01
ExAC Global Study-wide 20422 T=0.98639 C=0.01361
ExAC Europe Sub 8908 T=0.9791 C=0.0209
ExAC Asian Sub 8608 T=0.9920 C=0.0080
ExAC African Sub 2264 T=0.9938 C=0.0062
ExAC American Sub 446 T=0.984 C=0.016
ExAC Other Sub 196 T=0.990 C=0.010
8.3KJPN JAPANESE Study-wide 16760 T=0.99988 C=0.00012
1000Genomes_30x Global Study-wide 6404 T=0.9905 C=0.0095
1000Genomes_30x African Sub 1786 T=0.9978 C=0.0022
1000Genomes_30x Europe Sub 1266 T=0.9755 C=0.0245
1000Genomes_30x South Asian Sub 1202 T=0.9950 C=0.0050
1000Genomes_30x East Asian Sub 1170 T=1.0000 C=0.0000
1000Genomes_30x American Sub 980 T=0.980 C=0.020
1000Genomes Global Study-wide 5008 T=0.9906 C=0.0094
1000Genomes African Sub 1322 T=0.9977 C=0.0023
1000Genomes East Asian Sub 1008 T=1.0000 C=0.0000
1000Genomes Europe Sub 1006 T=0.9751 C=0.0249
1000Genomes South Asian Sub 978 T=0.996 C=0.004
1000Genomes American Sub 694 T=0.978 C=0.022
GO Exome Sequencing Project Global Study-wide 4566 T=0.9823 C=0.0177
GO Exome Sequencing Project European American Sub 3182 T=0.9761 C=0.0239
GO Exome Sequencing Project African American Sub 1384 T=0.9964 C=0.0036
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.9946 C=0.0054
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.9800 C=0.0200
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.9814 C=0.0186
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.985 C=0.015
Northern Sweden ACPOP Study-wide 600 T=0.992 C=0.008
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 T=0.979 C=0.021
Qatari Global Study-wide 216 T=0.968 C=0.032
The Danish reference pan genome Danish Study-wide 40 T=0.97 C=0.03
SGDP_PRJ Global Study-wide 12 T=0.50 C=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 19 NC_000019.10:g.35119133T>C
GRCh37.p13 chr 19 NC_000019.9:g.35610037T>C
Gene: FXYD3, FXYD domain containing ion transport regulator 3 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
FXYD3 transcript variant 3 NM_001136007.2:c.74-35T>C N/A Intron Variant
FXYD3 transcript variant 4 NM_001136008.2:c.-14-230T…

NM_001136008.2:c.-14-230T>C

N/A Intron Variant
FXYD3 transcript variant 5 NM_001136009.2:c.-98-35T>C N/A Intron Variant
FXYD3 transcript variant 6 NM_001136010.2:c.-14-230T…

NM_001136010.2:c.-14-230T>C

N/A Intron Variant
FXYD3 transcript variant 7 NM_001136011.2:c.-98-35T>C N/A Intron Variant
FXYD3 transcript variant 8 NM_001136012.2:c.-14-230T…

NM_001136012.2:c.-14-230T>C

N/A Intron Variant
FXYD3 transcript variant 9 NM_001387349.1:c.-98-35T>C N/A Intron Variant
FXYD3 transcript variant 10 NM_001387350.1:c.-14-230T…

NM_001387350.1:c.-14-230T>C

N/A Intron Variant
FXYD3 transcript variant 11 NM_001387352.1:c.-98-35T>C N/A Intron Variant
FXYD3 transcript variant 12 NM_001387353.1:c.-14-230T…

NM_001387353.1:c.-14-230T>C

N/A Intron Variant
FXYD3 transcript variant 13 NM_001387354.1:c.-98-35T>C N/A Intron Variant
FXYD3 transcript variant 14 NM_001387355.1:c.74-230T>C N/A Intron Variant
FXYD3 transcript variant 1 NM_005971.4:c.-14-230T>C N/A Intron Variant
FXYD3 transcript variant 2 NM_021910.3:c.-98-35T>C 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 T= C
GRCh38.p14 chr 19 NC_000019.10:g.35119133= NC_000019.10:g.35119133T>C
GRCh37.p13 chr 19 NC_000019.9:g.35610037= NC_000019.9:g.35610037T>C
FXYD3 transcript variant 3 NM_001136007.1:c.74-35= NM_001136007.1:c.74-35T>C
FXYD3 transcript variant 3 NM_001136007.2:c.74-35= NM_001136007.2:c.74-35T>C
FXYD3 transcript variant 4 NM_001136008.1:c.-14-230= NM_001136008.1:c.-14-230T>C
FXYD3 transcript variant 4 NM_001136008.2:c.-14-230= NM_001136008.2:c.-14-230T>C
FXYD3 transcript variant 5 NM_001136009.1:c.-98-35= NM_001136009.1:c.-98-35T>C
FXYD3 transcript variant 5 NM_001136009.2:c.-98-35= NM_001136009.2:c.-98-35T>C
FXYD3 transcript variant 6 NM_001136010.1:c.-14-230= NM_001136010.1:c.-14-230T>C
FXYD3 transcript variant 6 NM_001136010.2:c.-14-230= NM_001136010.2:c.-14-230T>C
FXYD3 transcript variant 7 NM_001136011.1:c.-98-35= NM_001136011.1:c.-98-35T>C
FXYD3 transcript variant 7 NM_001136011.2:c.-98-35= NM_001136011.2:c.-98-35T>C
FXYD3 transcript variant 8 NM_001136012.1:c.-14-230= NM_001136012.1:c.-14-230T>C
FXYD3 transcript variant 8 NM_001136012.2:c.-14-230= NM_001136012.2:c.-14-230T>C
FXYD3 transcript variant 9 NM_001387349.1:c.-98-35= NM_001387349.1:c.-98-35T>C
FXYD3 transcript variant 10 NM_001387350.1:c.-14-230= NM_001387350.1:c.-14-230T>C
FXYD3 transcript variant 11 NM_001387352.1:c.-98-35= NM_001387352.1:c.-98-35T>C
FXYD3 transcript variant 12 NM_001387353.1:c.-14-230= NM_001387353.1:c.-14-230T>C
FXYD3 transcript variant 13 NM_001387354.1:c.-98-35= NM_001387354.1:c.-98-35T>C
FXYD3 transcript variant 14 NM_001387355.1:c.74-230= NM_001387355.1:c.74-230T>C
FXYD3 transcript variant 1 NM_005971.3:c.-14-230= NM_005971.3:c.-14-230T>C
FXYD3 transcript variant 1 NM_005971.4:c.-14-230= NM_005971.4:c.-14-230T>C
FXYD3 transcript variant 2 NM_021910.2:c.-98-35= NM_021910.2:c.-98-35T>C
FXYD3 transcript variant 2 NM_021910.3:c.-98-35= NM_021910.3:c.-98-35T>C
FXYD3 transcript variant X1 XM_005258992.1:c.146-35= XM_005258992.1:c.146-35T>C
FXYD3 transcript variant X2 XM_005258993.1:c.200-35= XM_005258993.1:c.200-35T>C
FXYD3 transcript variant X3 XM_005258994.1:c.146-35= XM_005258994.1:c.146-35T>C
FXYD3 transcript variant X4 XM_005258995.1:c.146-230= XM_005258995.1:c.146-230T>C
FXYD3 transcript variant X5 XM_005258996.1:c.-14-230= XM_005258996.1:c.-14-230T>C
FXYD3 transcript variant X6 XM_005258997.1:c.-14-230= XM_005258997.1:c.-14-230T>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#.

45 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss237666903 Jul 15, 2010 (132)
2 BL ss255651853 May 09, 2011 (134)
3 ILLUMINA ss532764658 Sep 08, 2015 (146)
4 NHLBI-ESP ss713502330 Apr 25, 2013 (138)
5 EVA-GONL ss994266441 Aug 21, 2014 (142)
6 JMKIDD_LAB ss1081881826 Aug 21, 2014 (142)
7 1000GENOMES ss1363036468 Aug 21, 2014 (142)
8 EVA_GENOME_DK ss1578627597 Apr 01, 2015 (144)
9 EVA_UK10K_ALSPAC ss1637905400 Apr 01, 2015 (144)
10 EVA_UK10K_TWINSUK ss1680899433 Apr 01, 2015 (144)
11 EVA_EXAC ss1693534913 Apr 01, 2015 (144)
12 EVA_DECODE ss1698320036 Apr 01, 2015 (144)
13 EVA_MGP ss1711509801 Apr 01, 2015 (144)
14 WEILL_CORNELL_DGM ss1937760121 Feb 12, 2016 (147)
15 JJLAB ss2029657862 Sep 14, 2016 (149)
16 HUMAN_LONGEVITY ss2225510533 Dec 20, 2016 (150)
17 GNOMAD ss2743889689 Nov 08, 2017 (151)
18 GNOMAD ss2750154783 Nov 08, 2017 (151)
19 GNOMAD ss2962479031 Nov 08, 2017 (151)
20 SWEGEN ss3017413746 Nov 08, 2017 (151)
21 ILLUMINA ss3627924371 Oct 12, 2018 (152)
22 EGCUT_WGS ss3684189168 Jul 13, 2019 (153)
23 EVA_DECODE ss3702701560 Jul 13, 2019 (153)
24 ACPOP ss3743009914 Jul 13, 2019 (153)
25 KHV_HUMAN_GENOMES ss3821273179 Jul 13, 2019 (153)
26 EVA ss3825274185 Apr 27, 2020 (154)
27 SGDP_PRJ ss3888146740 Apr 27, 2020 (154)
28 FSA-LAB ss3984151744 Apr 27, 2021 (155)
29 EVA ss3986792279 Apr 27, 2021 (155)
30 TOPMED ss5073716933 Apr 27, 2021 (155)
31 TOMMO_GENOMICS ss5227590016 Apr 27, 2021 (155)
32 1000G_HIGH_COVERAGE ss5307128106 Oct 16, 2022 (156)
33 EVA ss5434635282 Oct 16, 2022 (156)
34 HUGCELL_USP ss5499669528 Oct 16, 2022 (156)
35 1000G_HIGH_COVERAGE ss5612806122 Oct 16, 2022 (156)
36 SANFORD_IMAGENETICS ss5624428040 Oct 16, 2022 (156)
37 SANFORD_IMAGENETICS ss5662326111 Oct 16, 2022 (156)
38 TOMMO_GENOMICS ss5786167651 Oct 16, 2022 (156)
39 EVA ss5840504390 Oct 16, 2022 (156)
40 EVA ss5847496555 Oct 16, 2022 (156)
41 EVA ss5847842156 Oct 16, 2022 (156)
42 EVA ss5848489734 Oct 16, 2022 (156)
43 EVA ss5927976741 Oct 16, 2022 (156)
44 EVA ss5953742078 Oct 16, 2022 (156)
45 EVA ss5979545100 Oct 16, 2022 (156)
46 1000Genomes NC_000019.9 - 35610037 Oct 12, 2018 (152)
47 1000Genomes_30x NC_000019.10 - 35119133 Oct 16, 2022 (156)
48 The Avon Longitudinal Study of Parents and Children NC_000019.9 - 35610037 Oct 12, 2018 (152)
49 Genetic variation in the Estonian population NC_000019.9 - 35610037 Oct 12, 2018 (152)
50 ExAC NC_000019.9 - 35610037 Oct 12, 2018 (152)
51 The Danish reference pan genome NC_000019.9 - 35610037 Apr 27, 2020 (154)
52 gnomAD - Genomes NC_000019.10 - 35119133 Apr 27, 2021 (155)
53 gnomAD - Exomes NC_000019.9 - 35610037 Jul 13, 2019 (153)
54 GO Exome Sequencing Project NC_000019.9 - 35610037 Oct 12, 2018 (152)
55 Genome of the Netherlands Release 5 NC_000019.9 - 35610037 Apr 27, 2020 (154)
56 Medical Genome Project healthy controls from Spanish population NC_000019.9 - 35610037 Apr 27, 2020 (154)
57 Northern Sweden NC_000019.9 - 35610037 Jul 13, 2019 (153)
58 Qatari NC_000019.9 - 35610037 Apr 27, 2020 (154)
59 SGDP_PRJ NC_000019.9 - 35610037 Apr 27, 2020 (154)
60 8.3KJPN NC_000019.9 - 35610037 Apr 27, 2021 (155)
61 14KJPN NC_000019.10 - 35119133 Oct 16, 2022 (156)
62 TopMed NC_000019.10 - 35119133 Apr 27, 2021 (155)
63 UK 10K study - Twins NC_000019.9 - 35610037 Oct 12, 2018 (152)
64 ALFA NC_000019.10 - 35119133 Apr 27, 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
ss255651853, ss1698320036 NC_000019.8:40301876:T:C NC_000019.10:35119132:T:C (self)
76438854, 42339672, 29927416, 4034774, 4810628, 13203479, 1731152, 18862258, 625561, 16294779, 19802043, 40163720, 85559323, 42339672, ss237666903, ss532764658, ss713502330, ss994266441, ss1081881826, ss1363036468, ss1578627597, ss1637905400, ss1680899433, ss1693534913, ss1711509801, ss1937760121, ss2029657862, ss2743889689, ss2750154783, ss2962479031, ss3017413746, ss3627924371, ss3684189168, ss3743009914, ss3825274185, ss3888146740, ss3984151744, ss3986792279, ss5227590016, ss5434635282, ss5624428040, ss5662326111, ss5840504390, ss5847496555, ss5847842156, ss5848489734, ss5953742078, ss5979545100 NC_000019.9:35610036:T:C NC_000019.10:35119132:T:C (self)
100332057, 539085093, 120004755, 289262597, 1094921109, ss2225510533, ss3702701560, ss3821273179, ss5073716933, ss5307128106, ss5499669528, ss5612806122, ss5786167651, ss5927976741 NC_000019.10:35119132:T:C NC_000019.10:35119132:T: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 rs80021793

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