Name: rs577912
Published: September 21, 2022
License: Open Access

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.

rs577912

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr13:33036014 (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>G
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.170728 (45190/264690, TOPMED)
T=0.168939 (23667/140092, GnomAD)
T=0.23448 (6626/28258, 14KJPN) (+ 17 more)
T=0.15874 (3798/23926, ALFA)
T=0.23365 (3916/16760, 8.3KJPN)
T=0.1974 (1264/6404, 1000G_30x)
T=0.1953 (978/5008, 1000G)
T=0.1542 (691/4480, Estonian)
T=0.1565 (603/3854, ALSPAC)
T=0.1448 (537/3708, TWINSUK)
T=0.2324 (681/2930, KOREAN)
T=0.2045 (387/1892, HapMap)
T=0.170 (170/998, GoNL)
T=0.196 (155/792, PRJEB37584)
T=0.200 (120/600, NorthernSweden)
T=0.131 (71/542, SGDP_PRJ)
T=0.134 (29/216, Qatari)
T=0.364 (78/214, Vietnamese)
T=0.09 (5/54, Siberian)
T=0.17 (7/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: KL : Intron Variant
Publications: 4 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	23926	T=0.15874	G=0.84126
European	Sub	15648	T=0.15350	G=0.84650
African	Sub	3612	T=0.2279	G=0.7721
African Others	Sub	126	T=0.222	G=0.778
African American	Sub	3486	T=0.2281	G=0.7719
Asian	Sub	158	T=0.329	G=0.671
East Asian	Sub	102	T=0.284	G=0.716
Other Asian	Sub	56	T=0.41	G=0.59
Latin American 1	Sub	292	T=0.168	G=0.832
Latin American 2	Sub	2766	T=0.0980	G=0.9020
South Asian	Sub	110	T=0.118	G=0.882
Other	Sub	1340	T=0.1403	G=0.8597

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").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	T=0.170728	G=0.829272
gnomAD - Genomes	Global	Study-wide	140092	T=0.168939	G=0.831061
gnomAD - Genomes	European	Sub	75886	T=0.14088	G=0.85912
gnomAD - Genomes	African	Sub	41960	T=0.22917	G=0.77083
gnomAD - Genomes	American	Sub	13650	T=0.13136	G=0.86864
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	T=0.0933	G=0.9067
gnomAD - Genomes	East Asian	Sub	3118	T=0.2886	G=0.7114
gnomAD - Genomes	Other	Sub	2154	T=0.1657	G=0.8343
14KJPN	JAPANESE	Study-wide	28258	T=0.23448	G=0.76552
Allele Frequency Aggregator	Total	Global	23926	T=0.15874	G=0.84126
Allele Frequency Aggregator	European	Sub	15648	T=0.15350	G=0.84650
Allele Frequency Aggregator	African	Sub	3612	T=0.2279	G=0.7721
Allele Frequency Aggregator	Latin American 2	Sub	2766	T=0.0980	G=0.9020
Allele Frequency Aggregator	Other	Sub	1340	T=0.1403	G=0.8597
Allele Frequency Aggregator	Latin American 1	Sub	292	T=0.168	G=0.832
Allele Frequency Aggregator	Asian	Sub	158	T=0.329	G=0.671
Allele Frequency Aggregator	South Asian	Sub	110	T=0.118	G=0.882
8.3KJPN	JAPANESE	Study-wide	16760	T=0.23365	G=0.76635
1000Genomes_30x	Global	Study-wide	6404	T=0.1974	G=0.8026
1000Genomes_30x	African	Sub	1786	T=0.2430	G=0.7570
1000Genomes_30x	Europe	Sub	1266	T=0.1295	G=0.8705
1000Genomes_30x	South Asian	Sub	1202	T=0.1872	G=0.8128
1000Genomes_30x	East Asian	Sub	1170	T=0.2846	G=0.7154
1000Genomes_30x	American	Sub	980	T=0.110	G=0.890
1000Genomes	Global	Study-wide	5008	T=0.1953	G=0.8047
1000Genomes	African	Sub	1322	T=0.2390	G=0.7610
1000Genomes	East Asian	Sub	1008	T=0.2827	G=0.7173
1000Genomes	Europe	Sub	1006	T=0.1233	G=0.8767
1000Genomes	South Asian	Sub	978	T=0.182	G=0.818
1000Genomes	American	Sub	694	T=0.108	G=0.892
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.1542	G=0.8458
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.1565	G=0.8435
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.1448	G=0.8552
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.2324	G=0.7676
HapMap	Global	Study-wide	1892	T=0.2045	G=0.7955
HapMap	American	Sub	770	T=0.165	G=0.835
HapMap	African	Sub	692	T=0.264	G=0.736
HapMap	Asian	Sub	254	T=0.236	G=0.764
HapMap	Europe	Sub	176	T=0.097	G=0.903
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.170	G=0.830
CNV burdens in cranial meningiomas	Global	Study-wide	792	T=0.196	G=0.804
CNV burdens in cranial meningiomas	CRM	Sub	792	T=0.196	G=0.804
Northern Sweden	ACPOP	Study-wide	600	T=0.200	G=0.800
SGDP_PRJ	Global	Study-wide	542	T=0.131	G=0.869
Qatari	Global	Study-wide	216	T=0.134	G=0.866
A Vietnamese Genetic Variation Database	Global	Study-wide	214	T=0.364	G=0.636
Siberian	Global	Study-wide	54	T=0.09	G=0.91
The Danish reference pan genome	Danish	Study-wide	40	T=0.17	G=0.82

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 13	NC_000013.11:g.33036014T>G
GRCh37.p13 chr 13	NC_000013.10:g.33610151T>G
KL RefSeqGene	NG_011485.2:g.24773T>G
KL RefSeqGene	NG_011485.1:g.24581T>G

Gene: KL, klotho (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
KL transcript	NM_004795.4:c.820-17753T>G	N/A	Intron Variant
KL transcript variant X1	XM_006719895.3:c.-102-177… XM_006719895.3:c.-102-17753T>G	N/A	Intron Variant
KL transcript variant X2	XM_047430775.1:c.820-1775… XM_047430775.1:c.820-17753T>G	N/A	Intron Variant
KL transcript variant X3	XM_047430776.1:c.820-1775… XM_047430776.1:c.820-17753T>G	N/A	Intron Variant

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

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=	G
GRCh38.p14 chr 13	NC_000013.11:g.33036014=	NC_000013.11:g.33036014T>G
GRCh37.p13 chr 13	NC_000013.10:g.33610151=	NC_000013.10:g.33610151T>G
KL RefSeqGene	NG_011485.2:g.24773=	NG_011485.2:g.24773T>G
KL RefSeqGene	NG_011485.1:g.24581=	NG_011485.1:g.24581T>G
KL transcript	NM_004795.3:c.820-17753=	NM_004795.3:c.820-17753T>G
KL transcript	NM_004795.4:c.820-17753=	NM_004795.4:c.820-17753T>G
KL transcript variant X1	XM_006719895.3:c.-102-17753=	XM_006719895.3:c.-102-17753T>G
KL transcript variant X2	XM_047430775.1:c.820-17753=	XM_047430775.1:c.820-17753T>G
KL transcript variant X3	XM_047430776.1:c.820-17753=	XM_047430776.1:c.820-17753T>G

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#.

85 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss749376	Aug 11, 2000 (83)
2	KWOK	ss993958	Oct 04, 2000 (86)
3	KWOK	ss1706457	Oct 18, 2000 (87)
4	KWOK	ss1739038	Oct 18, 2000 (87)
5	WI_SSAHASNP	ss12262847	Jul 11, 2003 (116)
6	SC_SNP	ss13222495	Dec 05, 2003 (119)
7	SSAHASNP	ss21108452	Apr 05, 2004 (121)
8	AFFY	ss76661502	Dec 07, 2007 (129)
9	HGSV	ss77365921	Dec 07, 2007 (129)
10	HGSV	ss78256708	Dec 07, 2007 (129)
11	HGSV	ss85201285	Dec 15, 2007 (130)
12	BCMHGSC_JDW	ss89582045	Mar 24, 2008 (129)
13	HUMANGENOME_JCVI	ss96957524	Feb 06, 2009 (130)
14	BGI	ss103109446	Dec 01, 2009 (131)
15	KRIBB_YJKIM	ss104821161	Feb 06, 2009 (130)
16	1000GENOMES	ss112676158	Jan 25, 2009 (130)
17	1000GENOMES	ss114515858	Jan 25, 2009 (130)
18	ILLUMINA-UK	ss118414561	Feb 14, 2009 (130)
19	ENSEMBL	ss133523614	Dec 01, 2009 (131)
20	ENSEMBL	ss137263137	Dec 01, 2009 (131)
21	GMI	ss154632811	Dec 01, 2009 (131)
22	COMPLETE_GENOMICS	ss167864416	Jul 04, 2010 (132)
23	COMPLETE_GENOMICS	ss169171125	Jul 04, 2010 (132)
24	COMPLETE_GENOMICS	ss170984406	Jul 04, 2010 (132)
25	BUSHMAN	ss199056467	Jul 04, 2010 (132)
26	BCM-HGSC-SUB	ss208518994	Jul 04, 2010 (132)
27	1000GENOMES	ss226118423	Jul 14, 2010 (132)
28	1000GENOMES	ss236203977	Jul 15, 2010 (132)
29	1000GENOMES	ss242708486	Jul 15, 2010 (132)
30	ILLUMINA	ss244303624	Jul 04, 2010 (132)
31	GMI	ss281665810	May 04, 2012 (137)
32	GMI	ss286682026	Apr 25, 2013 (138)
33	PJP	ss291572579	May 09, 2011 (134)
34	TISHKOFF	ss563593126	Apr 25, 2013 (138)
35	SSMP	ss659189603	Apr 25, 2013 (138)
36	EVA-GONL	ss990263355	Aug 21, 2014 (142)
37	JMKIDD_LAB	ss1078989578	Aug 21, 2014 (142)
38	1000GENOMES	ss1347747967	Aug 21, 2014 (142)
39	DDI	ss1427150937	Apr 01, 2015 (144)
40	EVA_GENOME_DK	ss1576715985	Apr 01, 2015 (144)
41	EVA_UK10K_ALSPAC	ss1630027413	Apr 01, 2015 (144)
42	EVA_DECODE	ss1642367754	Apr 01, 2015 (144)
43	EVA_UK10K_TWINSUK	ss1673021446	Apr 01, 2015 (144)
44	EVA_SVP	ss1713381359	Apr 01, 2015 (144)
45	HAMMER_LAB	ss1807557122	Sep 08, 2015 (146)
46	WEILL_CORNELL_DGM	ss1933632215	Feb 12, 2016 (147)
47	GENOMED	ss1967752258	Jul 19, 2016 (147)
48	JJLAB	ss2027573366	Sep 14, 2016 (149)
49	USC_VALOUEV	ss2155937792	Dec 20, 2016 (150)
50	HUMAN_LONGEVITY	ss2195365150	Dec 20, 2016 (150)
51	SYSTEMSBIOZJU	ss2628274811	Nov 08, 2017 (151)
52	GRF	ss2700310704	Nov 08, 2017 (151)
53	GNOMAD	ss2918301986	Nov 08, 2017 (151)
54	SWEGEN	ss3010826566	Nov 08, 2017 (151)
55	BIOINF_KMB_FNS_UNIBA	ss3027602611	Nov 08, 2017 (151)
56	CSHL	ss3350397969	Nov 08, 2017 (151)
57	URBANLAB	ss3650005031	Oct 12, 2018 (152)
58	EGCUT_WGS	ss3678088296	Jul 13, 2019 (153)
59	EVA_DECODE	ss3695055658	Jul 13, 2019 (153)
60	ACPOP	ss3739641100	Jul 13, 2019 (153)
61	EVA	ss3751316476	Jul 13, 2019 (153)
62	PACBIO	ss3787423697	Jul 13, 2019 (153)
63	PACBIO	ss3792495104	Jul 13, 2019 (153)
64	PACBIO	ss3797378857	Jul 13, 2019 (153)
65	KHV_HUMAN_GENOMES	ss3816646979	Jul 13, 2019 (153)
66	EVA	ss3833484189	Apr 27, 2020 (154)
67	EVA	ss3840320307	Apr 27, 2020 (154)
68	EVA	ss3845805284	Apr 27, 2020 (154)
69	SGDP_PRJ	ss3879727101	Apr 27, 2020 (154)
70	KRGDB	ss3928555921	Apr 27, 2020 (154)
71	EVA	ss3984678374	Apr 26, 2021 (155)
72	TOPMED	ss4942105610	Apr 26, 2021 (155)
73	TOMMO_GENOMICS	ss5209459706	Apr 26, 2021 (155)
74	1000G_HIGH_COVERAGE	ss5293319717	Oct 16, 2022 (156)
75	EVA	ss5410010587	Oct 16, 2022 (156)
76	HUGCELL_USP	ss5487724498	Oct 16, 2022 (156)
77	EVA	ss5510929694	Oct 16, 2022 (156)
78	1000G_HIGH_COVERAGE	ss5592058396	Oct 16, 2022 (156)
79	SANFORD_IMAGENETICS	ss5654530368	Oct 16, 2022 (156)
80	TOMMO_GENOMICS	ss5761182911	Oct 16, 2022 (156)
81	YY_MCH	ss5814006576	Oct 16, 2022 (156)
82	EVA	ss5839311157	Oct 16, 2022 (156)
83	EVA	ss5850675440	Oct 16, 2022 (156)
84	EVA	ss5924627874	Oct 16, 2022 (156)
85	EVA	ss5945940556	Oct 16, 2022 (156)
86	1000Genomes	NC_000013.10 - 33610151	Oct 12, 2018 (152)
87	1000Genomes_30x	NC_000013.11 - 33036014	Oct 16, 2022 (156)
88	The Avon Longitudinal Study of Parents and Children	NC_000013.10 - 33610151	Oct 12, 2018 (152)
89	Genetic variation in the Estonian population	NC_000013.10 - 33610151	Oct 12, 2018 (152)
90	The Danish reference pan genome	NC_000013.10 - 33610151	Apr 27, 2020 (154)
91	gnomAD - Genomes	NC_000013.11 - 33036014	Apr 26, 2021 (155)
92	Genome of the Netherlands Release 5	NC_000013.10 - 33610151	Apr 27, 2020 (154)
93	HapMap	NC_000013.11 - 33036014	Apr 27, 2020 (154)
94	KOREAN population from KRGDB	NC_000013.10 - 33610151	Apr 27, 2020 (154)
95	Northern Sweden	NC_000013.10 - 33610151	Jul 13, 2019 (153)
96	CNV burdens in cranial meningiomas	NC_000013.10 - 33610151	Apr 26, 2021 (155)
97	Qatari	NC_000013.10 - 33610151	Apr 27, 2020 (154)
98	SGDP_PRJ	NC_000013.10 - 33610151	Apr 27, 2020 (154)
99	Siberian	NC_000013.10 - 33610151	Apr 27, 2020 (154)
100	8.3KJPN	NC_000013.10 - 33610151	Apr 26, 2021 (155)
101	14KJPN	NC_000013.11 - 33036014	Oct 16, 2022 (156)
102	TopMed	NC_000013.11 - 33036014	Apr 26, 2021 (155)
103	UK 10K study - Twins	NC_000013.10 - 33610151	Oct 12, 2018 (152)
104	A Vietnamese Genetic Variation Database	NC_000013.10 - 33610151	Jul 13, 2019 (153)
105	ALFA	NC_000013.11 - 33036014	Apr 26, 2021 (155)

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).

Associated ID	History Updated (Build)
rs60279845	May 25, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss76661502, ss77365921, ss78256708, ss85201285, ss89582045, ss112676158, ss114515858, ss118414561, ss167864416, ss169171125, ss170984406, ss199056467, ss208518994, ss244303624, ss281665810, ss286682026, ss291572579, ss1642367754, ss1713381359	NC_000013.9:32508150:T:G	NC_000013.11:33036013:T:G	(self)
60601198, 33661154, 23826544, 3249000, 15018941, 35733315, 12925965, 227878, 15674145, 31744081, 8454146, 67429013, 33661154, 7466470, ss226118423, ss236203977, ss242708486, ss563593126, ss659189603, ss990263355, ss1078989578, ss1347747967, ss1427150937, ss1576715985, ss1630027413, ss1673021446, ss1807557122, ss1933632215, ss1967752258, ss2027573366, ss2155937792, ss2628274811, ss2700310704, ss2918301986, ss3010826566, ss3350397969, ss3678088296, ss3739641100, ss3751316476, ss3787423697, ss3792495104, ss3797378857, ss3833484189, ss3840320307, ss3879727101, ss3928555921, ss3984678374, ss5209459706, ss5410010587, ss5510929694, ss5654530368, ss5839311157, ss5945940556	NC_000013.10:33610150:T:G	NC_000013.11:33036013:T:G	(self)
79584331, 427298798, 963008, 95020015, 157651268, 7031521647, ss2195365150, ss3027602611, ss3650005031, ss3695055658, ss3816646979, ss3845805284, ss4942105610, ss5293319717, ss5487724498, ss5592058396, ss5761182911, ss5814006576, ss5850675440, ss5924627874	NC_000013.11:33036013:T:G	NC_000013.11:33036013:T:G	(self)
ss12262847, ss13222495	NT_024524.12:2184641:T:G	NC_000013.11:33036013:T:G	(self)
ss21108452	NT_024524.13:14590150:T:G	NC_000013.11:33036013:T:G	(self)
ss749376, ss993958, ss1706457, ss1739038, ss96957524, ss103109446, ss104821161, ss133523614, ss137263137, ss154632811	NT_024524.14:14590150:T:G	NC_000013.11:33036013:T:G	(self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

4 citations for rs577912

PMID	Title	Author	Year	Journal
19419323	Klotho variants and chronic hemodialysis mortality.	Friedman DJ et al.	2009	Journal of bone and mineral research
20401335	Sickle Cell Disease in the Post Genomic Era: A Monogenic Disease with a Polygenic Phenotype.	Driss A et al.	2009	Genomics insights
23756195	Klotho gene polymorphism of rs3752472 is associated with the risk of urinary calculi in the population of Han nationality in Eastern China.	Xu C et al.	2013	Gene
35205271	MIF rs755622 and IL6 rs1800795 Are Implied in Genetic Susceptibility to End-Stage Renal Disease (ESRD).	Guarneri M et al.	2022	Genes

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs577912