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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.

rs12977772

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr19:18564335 (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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.132706 (35126/264690, TOPMED)
T=0.135478 (18964/139978, GnomAD)
T=0.15872 (6408/40372, ALFA) (+ 16 more)
T=0.00357 (101/28258, 14KJPN)
T=0.00328 (55/16760, 8.3KJPN)
T=0.1162 (744/6404, 1000G_30x)
T=0.1140 (571/5008, 1000G)
T=0.1458 (653/4480, Estonian)
T=0.1816 (700/3854, ALSPAC)
T=0.1839 (682/3708, TWINSUK)
T=0.0038 (11/2922, KOREAN)
T=0.0038 (7/1832, Korea1K)
T=0.154 (154/998, GoNL)
T=0.148 (89/600, NorthernSweden)
T=0.213 (46/216, Qatari)
T=0.023 (5/214, Vietnamese)
G=0.454 (49/108, SGDP_PRJ)
T=0.17 (7/40, GENOME_DK)
G=0.33 (4/12, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
UBA52 : Intron Variant
KXD1 : 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 40466 G=0.84125 T=0.15875
European Sub 30916 G=0.81932 T=0.18068
African Sub 6220 G=0.9574 T=0.0426
African Others Sub 208 G=0.981 T=0.019
African American Sub 6012 G=0.9566 T=0.0434
Asian Sub 128 G=0.945 T=0.055
East Asian Sub 100 G=0.97 T=0.03
Other Asian Sub 28 G=0.86 T=0.14
Latin American 1 Sub 168 G=0.821 T=0.179
Latin American 2 Sub 700 G=0.824 T=0.176
South Asian Sub 114 G=0.772 T=0.228
Other Sub 2220 G=0.8257 T=0.1743


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=0.867294 T=0.132706
gnomAD - Genomes Global Study-wide 139978 G=0.864522 T=0.135478
gnomAD - Genomes European Sub 75816 G=0.82051 T=0.17949
gnomAD - Genomes African Sub 41970 G=0.96011 T=0.03989
gnomAD - Genomes American Sub 13596 G=0.81789 T=0.18211
gnomAD - Genomes Ashkenazi Jewish Sub 3318 G=0.7474 T=0.2526
gnomAD - Genomes East Asian Sub 3134 G=0.9853 T=0.0147
gnomAD - Genomes Other Sub 2144 G=0.8498 T=0.1502
Allele Frequency Aggregator Total Global 40372 G=0.84128 T=0.15872
Allele Frequency Aggregator European Sub 30840 G=0.81936 T=0.18064
Allele Frequency Aggregator African Sub 6220 G=0.9574 T=0.0426
Allele Frequency Aggregator Other Sub 2202 G=0.8247 T=0.1753
Allele Frequency Aggregator Latin American 2 Sub 700 G=0.824 T=0.176
Allele Frequency Aggregator Latin American 1 Sub 168 G=0.821 T=0.179
Allele Frequency Aggregator Asian Sub 128 G=0.945 T=0.055
Allele Frequency Aggregator South Asian Sub 114 G=0.772 T=0.228
14KJPN JAPANESE Study-wide 28258 G=0.99643 T=0.00357
8.3KJPN JAPANESE Study-wide 16760 G=0.99672 T=0.00328
1000Genomes_30x Global Study-wide 6404 G=0.8838 T=0.1162
1000Genomes_30x African Sub 1786 G=0.9815 T=0.0185
1000Genomes_30x Europe Sub 1266 G=0.7899 T=0.2101
1000Genomes_30x South Asian Sub 1202 G=0.8078 T=0.1922
1000Genomes_30x East Asian Sub 1170 G=0.9863 T=0.0137
1000Genomes_30x American Sub 980 G=0.798 T=0.202
1000Genomes Global Study-wide 5008 G=0.8860 T=0.1140
1000Genomes African Sub 1322 G=0.9826 T=0.0174
1000Genomes East Asian Sub 1008 G=0.9861 T=0.0139
1000Genomes Europe Sub 1006 G=0.7893 T=0.2107
1000Genomes South Asian Sub 978 G=0.807 T=0.193
1000Genomes American Sub 694 G=0.808 T=0.192
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.8542 T=0.1458
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.8184 T=0.1816
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.8161 T=0.1839
KOREAN population from KRGDB KOREAN Study-wide 2922 G=0.9962 T=0.0038
Korean Genome Project KOREAN Study-wide 1832 G=0.9962 T=0.0038
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.846 T=0.154
Northern Sweden ACPOP Study-wide 600 G=0.852 T=0.148
Qatari Global Study-wide 216 G=0.787 T=0.213
A Vietnamese Genetic Variation Database Global Study-wide 214 G=0.977 T=0.023
SGDP_PRJ Global Study-wide 108 G=0.454 T=0.546
The Danish reference pan genome Danish Study-wide 40 G=0.82 T=0.17
Siberian Global Study-wide 12 G=0.33 T=0.67
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.18564335G>T
GRCh37.p13 chr 19 NC_000019.9:g.18675145G>T
Gene: KXD1, KxDL motif containing 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
KXD1 transcript variant 1 NM_001171948.2:c.102-534G…

NM_001171948.2:c.102-534G>T

N/A Intron Variant
KXD1 transcript variant 3 NM_001171949.2:c.102-534G…

NM_001171949.2:c.102-534G>T

N/A Intron Variant
KXD1 transcript variant 2 NM_024069.4:c.102-534G>T N/A Intron Variant
KXD1 transcript variant X7 XM_005260073.5:c.102-534G…

XM_005260073.5:c.102-534G>T

N/A Intron Variant
KXD1 transcript variant X2 XM_006722883.3:c.102-534G…

XM_006722883.3:c.102-534G>T

N/A Intron Variant
KXD1 transcript variant X1 XM_011528272.3:c.102-534G…

XM_011528272.3:c.102-534G>T

N/A Intron Variant
KXD1 transcript variant X3 XM_017027281.2:c.102-534G…

XM_017027281.2:c.102-534G>T

N/A Intron Variant
KXD1 transcript variant X8 XM_017027282.2:c.102-534G…

XM_017027282.2:c.102-534G>T

N/A Intron Variant
KXD1 transcript variant X4 XM_047439388.1:c.102-534G…

XM_047439388.1:c.102-534G>T

N/A Intron Variant
KXD1 transcript variant X5 XM_047439389.1:c.102-534G…

XM_047439389.1:c.102-534G>T

N/A Intron Variant
KXD1 transcript variant X6 XM_047439390.1:c.102-534G…

XM_047439390.1:c.102-534G>T

N/A Intron Variant
Gene: UBA52, ubiquitin A-52 residue ribosomal protein fusion product 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
UBA52 transcript variant 1 NM_001033930.3:c. N/A Genic Upstream Transcript Variant
UBA52 transcript variant 3 NM_001321017.2:c. N/A Genic Upstream Transcript Variant
UBA52 transcript variant 4 NM_001321018.2:c. N/A Genic Upstream Transcript Variant
UBA52 transcript variant 5 NM_001321019.2:c. N/A Genic Upstream Transcript Variant
UBA52 transcript variant 6 NM_001321020.2:c. N/A Genic Upstream Transcript Variant
UBA52 transcript variant 7 NM_001321021.1:c. N/A Genic Upstream Transcript Variant
UBA52 transcript variant 8 NM_001321022.2:c. N/A Genic Upstream Transcript Variant
UBA52 transcript variant 2 NM_003333.5:c. N/A Genic Upstream Transcript Variant
UBA52 transcript variant X5 XM_005260054.2:c.-9+556G>T N/A Intron Variant
UBA52 transcript variant X2 XM_005260052.3:c. N/A Genic Upstream Transcript Variant
UBA52 transcript variant X3 XM_005260053.4:c. N/A Genic Upstream Transcript Variant
UBA52 transcript variant X4 XM_006722871.3:c. N/A Genic Upstream Transcript Variant
UBA52 transcript variant X1 XM_017027198.2: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= T
GRCh38.p14 chr 19 NC_000019.10:g.18564335= NC_000019.10:g.18564335G>T
GRCh37.p13 chr 19 NC_000019.9:g.18675145= NC_000019.9:g.18675145G>T
KXD1 transcript variant 1 NM_001171948.1:c.102-534= NM_001171948.1:c.102-534G>T
KXD1 transcript variant 1 NM_001171948.2:c.102-534= NM_001171948.2:c.102-534G>T
KXD1 transcript variant 3 NM_001171949.1:c.102-534= NM_001171949.1:c.102-534G>T
KXD1 transcript variant 3 NM_001171949.2:c.102-534= NM_001171949.2:c.102-534G>T
KXD1 transcript variant 2 NM_024069.3:c.102-534= NM_024069.3:c.102-534G>T
KXD1 transcript variant 2 NM_024069.4:c.102-534= NM_024069.4:c.102-534G>T
UBA52 transcript variant X5 XM_005260054.1:c.-9+556= XM_005260054.1:c.-9+556G>T
UBA52 transcript variant X5 XM_005260054.2:c.-9+556= XM_005260054.2:c.-9+556G>T
KXD1 transcript variant X1 XM_005260072.1:c.102-534= XM_005260072.1:c.102-534G>T
KXD1 transcript variant X2 XM_005260073.1:c.102-534= XM_005260073.1:c.102-534G>T
KXD1 transcript variant X7 XM_005260073.5:c.102-534= XM_005260073.5:c.102-534G>T
KXD1 transcript variant X2 XM_006722883.3:c.102-534= XM_006722883.3:c.102-534G>T
KXD1 transcript variant X1 XM_011528272.3:c.102-534= XM_011528272.3:c.102-534G>T
KXD1 transcript variant X3 XM_017027281.2:c.102-534= XM_017027281.2:c.102-534G>T
KXD1 transcript variant X8 XM_017027282.2:c.102-534= XM_017027282.2:c.102-534G>T
KXD1 transcript variant X4 XM_047439388.1:c.102-534= XM_047439388.1:c.102-534G>T
KXD1 transcript variant X5 XM_047439389.1:c.102-534= XM_047439389.1:c.102-534G>T
KXD1 transcript variant X6 XM_047439390.1:c.102-534= XM_047439390.1:c.102-534G>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#.

72 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 SSAHASNP ss21528293 Apr 05, 2004 (121)
2 ABI ss40978514 Mar 14, 2006 (126)
3 BCMHGSC_JDW ss90920748 Mar 24, 2008 (129)
4 HUMANGENOME_JCVI ss96257379 Feb 05, 2009 (130)
5 1000GENOMES ss111157783 Jan 25, 2009 (130)
6 ENSEMBL ss136311593 Dec 01, 2009 (131)
7 ENSEMBL ss137582075 Dec 01, 2009 (131)
8 BUSHMAN ss203700033 Jul 04, 2010 (132)
9 1000GENOMES ss237622687 Jul 15, 2010 (132)
10 GMI ss287355612 Apr 25, 2013 (138)
11 ILLUMINA ss483331341 May 04, 2012 (137)
12 ILLUMINA ss483801830 May 04, 2012 (137)
13 ILLUMINA ss535545806 Sep 08, 2015 (146)
14 SSMP ss661749048 Apr 25, 2013 (138)
15 ILLUMINA ss780237244 Sep 08, 2015 (146)
16 ILLUMINA ss782108772 Sep 08, 2015 (146)
17 ILLUMINA ss835722597 Sep 08, 2015 (146)
18 EVA-GONL ss994150786 Aug 21, 2014 (142)
19 JMKIDD_LAB ss1081799042 Aug 21, 2014 (142)
20 1000GENOMES ss1362597444 Aug 21, 2014 (142)
21 DDI ss1428354918 Apr 01, 2015 (144)
22 EVA_GENOME_DK ss1578580738 Apr 01, 2015 (144)
23 EVA_UK10K_ALSPAC ss1637680870 Apr 01, 2015 (144)
24 EVA_UK10K_TWINSUK ss1680674903 Apr 01, 2015 (144)
25 EVA_DECODE ss1698210283 Apr 01, 2015 (144)
26 WEILL_CORNELL_DGM ss1937638165 Feb 12, 2016 (147)
27 JJLAB ss2029592580 Sep 14, 2016 (149)
28 USC_VALOUEV ss2158121137 Dec 20, 2016 (150)
29 HUMAN_LONGEVITY ss2224781042 Dec 20, 2016 (150)
30 ILLUMINA ss2633525281 Nov 08, 2017 (151)
31 GNOMAD ss2961186572 Nov 08, 2017 (151)
32 AFFY ss2985136589 Nov 08, 2017 (151)
33 AFFY ss2985769043 Nov 08, 2017 (151)
34 SWEGEN ss3017209454 Nov 08, 2017 (151)
35 ILLUMINA ss3021890912 Nov 08, 2017 (151)
36 BIOINF_KMB_FNS_UNIBA ss3028628863 Nov 08, 2017 (151)
37 CSHL ss3352228908 Nov 08, 2017 (151)
38 ILLUMINA ss3627904210 Oct 12, 2018 (152)
39 ILLUMINA ss3631497756 Oct 12, 2018 (152)
40 ILLUMINA ss3642053490 Oct 12, 2018 (152)
41 URBANLAB ss3650881362 Oct 12, 2018 (152)
42 ILLUMINA ss3652316357 Oct 12, 2018 (152)
43 ILLUMINA ss3653908574 Oct 12, 2018 (152)
44 EGCUT_WGS ss3684029692 Jul 13, 2019 (153)
45 EVA_DECODE ss3702477676 Jul 13, 2019 (153)
46 ILLUMINA ss3725716870 Jul 13, 2019 (153)
47 ACPOP ss3742911230 Jul 13, 2019 (153)
48 EVA ss3755885530 Jul 13, 2019 (153)
49 KHV_HUMAN_GENOMES ss3821139822 Jul 13, 2019 (153)
50 EVA ss3835386361 Apr 27, 2020 (154)
51 EVA ss3841313058 Apr 27, 2020 (154)
52 EVA ss3846817922 Apr 27, 2020 (154)
53 SGDP_PRJ ss3887902788 Apr 27, 2020 (154)
54 KRGDB ss3937908178 Apr 27, 2020 (154)
55 KOGIC ss3980994544 Apr 27, 2020 (154)
56 TOPMED ss5070038930 Apr 26, 2021 (155)
57 TOMMO_GENOMICS ss5227061163 Apr 26, 2021 (155)
58 EVA ss5237594905 Apr 26, 2021 (155)
59 1000G_HIGH_COVERAGE ss5306729609 Oct 16, 2022 (156)
60 EVA ss5315966319 Oct 16, 2022 (156)
61 EVA ss5433957029 Oct 16, 2022 (156)
62 HUGCELL_USP ss5499326136 Oct 16, 2022 (156)
63 1000G_HIGH_COVERAGE ss5612219437 Oct 16, 2022 (156)
64 SANFORD_IMAGENETICS ss5662103637 Oct 16, 2022 (156)
65 TOMMO_GENOMICS ss5785453903 Oct 16, 2022 (156)
66 YY_MCH ss5817463967 Oct 16, 2022 (156)
67 EVA ss5840345905 Oct 16, 2022 (156)
68 EVA ss5847494896 Oct 16, 2022 (156)
69 EVA ss5852230109 Oct 16, 2022 (156)
70 EVA ss5927543327 Oct 16, 2022 (156)
71 EVA ss5953520483 Oct 16, 2022 (156)
72 EVA ss5979542258 Oct 16, 2022 (156)
73 1000Genomes NC_000019.9 - 18675145 Oct 12, 2018 (152)
74 1000Genomes_30x NC_000019.10 - 18564335 Oct 16, 2022 (156)
75 The Avon Longitudinal Study of Parents and Children NC_000019.9 - 18675145 Oct 12, 2018 (152)
76 Genetic variation in the Estonian population NC_000019.9 - 18675145 Oct 12, 2018 (152)
77 The Danish reference pan genome NC_000019.9 - 18675145 Apr 27, 2020 (154)
78 gnomAD - Genomes NC_000019.10 - 18564335 Apr 26, 2021 (155)
79 Genome of the Netherlands Release 5 NC_000019.9 - 18675145 Apr 27, 2020 (154)
80 KOREAN population from KRGDB NC_000019.9 - 18675145 Apr 27, 2020 (154)
81 Korean Genome Project NC_000019.10 - 18564335 Apr 27, 2020 (154)
82 Northern Sweden NC_000019.9 - 18675145 Jul 13, 2019 (153)
83 Qatari NC_000019.9 - 18675145 Apr 27, 2020 (154)
84 SGDP_PRJ NC_000019.9 - 18675145 Apr 27, 2020 (154)
85 Siberian NC_000019.9 - 18675145 Apr 27, 2020 (154)
86 8.3KJPN NC_000019.9 - 18675145 Apr 26, 2021 (155)
87 14KJPN NC_000019.10 - 18564335 Oct 16, 2022 (156)
88 TopMed NC_000019.10 - 18564335 Apr 26, 2021 (155)
89 UK 10K study - Twins NC_000019.9 - 18675145 Oct 12, 2018 (152)
90 A Vietnamese Genetic Variation Database NC_000019.9 - 18675145 Jul 13, 2019 (153)
91 ALFA NC_000019.10 - 18564335 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
ss90920748, ss111157783, ss203700033, ss287355612, ss483801830, ss1698210283 NC_000019.8:18536144:G:T NC_000019.10:18564334:G:T (self)
75984582, 42091606, 29767940, 4765460, 18751270, 45085572, 16196095, 19680087, 39919768, 10637491, 85030470, 42091606, 9301441, ss237622687, ss483331341, ss535545806, ss661749048, ss780237244, ss782108772, ss835722597, ss994150786, ss1081799042, ss1362597444, ss1428354918, ss1578580738, ss1637680870, ss1680674903, ss1937638165, ss2029592580, ss2158121137, ss2633525281, ss2961186572, ss2985136589, ss2985769043, ss3017209454, ss3021890912, ss3352228908, ss3627904210, ss3631497756, ss3642053490, ss3652316357, ss3653908574, ss3684029692, ss3742911230, ss3755885530, ss3835386361, ss3841313058, ss3887902788, ss3937908178, ss5227061163, ss5237594905, ss5315966319, ss5433957029, ss5662103637, ss5840345905, ss5847494896, ss5953520483, ss5979542258 NC_000019.9:18675144:G:T NC_000019.10:18564334:G:T (self)
99745372, 535904830, 37372545, 119291007, 285584594, 3775006269, ss2224781042, ss3028628863, ss3650881362, ss3702477676, ss3725716870, ss3821139822, ss3846817922, ss3980994544, ss5070038930, ss5306729609, ss5499326136, ss5612219437, ss5785453903, ss5817463967, ss5852230109, ss5927543327 NC_000019.10:18564334:G:T NC_000019.10:18564334:G:T (self)
ss21528293 NT_011295.10:9937946:G:T NC_000019.10:18564334:G:T (self)
ss40978514, ss96257379, ss136311593, ss137582075 NT_011295.11:9937946:G:T NC_000019.10:18564334:G:T (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 rs12977772

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