Name: rs2062506
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.

rs2062506

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr12:122600289 (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: A>C / A>G
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.226514 (59956/264690, TOPMED)
A=0.217969 (30524/140038, GnomAD)
A=0.14697 (4153/28258, 14KJPN) (+ 16 more)
A=0.23637 (4465/18890, ALFA)
A=0.14356 (2406/16760, 8.3KJPN)
A=0.1818 (1164/6404, 1000G_30x)
A=0.1815 (909/5008, 1000G)
A=0.2359 (1057/4480, Estonian)
A=0.2649 (1021/3854, ALSPAC)
A=0.2654 (984/3708, TWINSUK)
A=0.1526 (447/2930, KOREAN)
A=0.1605 (294/1832, Korea1K)
A=0.230 (230/998, GoNL)
A=0.270 (162/600, NorthernSweden)
A=0.158 (84/532, SGDP_PRJ)
A=0.245 (53/216, Qatari)
A=0.203 (43/212, Vietnamese)
A=0.17 (9/54, Siberian)
A=0.25 (10/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: KNTC1 : 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	18890	A=0.23637	G=0.76363
European	Sub	14286	A=0.25479	G=0.74521
African	Sub	2946	A=0.1222	G=0.8778
African Others	Sub	114	A=0.132	G=0.868
African American	Sub	2832	A=0.1218	G=0.8782
Asian	Sub	112	A=0.170	G=0.830
East Asian	Sub	86	A=0.13	G=0.87
Other Asian	Sub	26	A=0.31	G=0.69
Latin American 1	Sub	146	A=0.260	G=0.740
Latin American 2	Sub	610	A=0.398	G=0.602
South Asian	Sub	98	A=0.14	G=0.86
Other	Sub	692	A=0.218	G=0.782

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	A=0.226514	G=0.773486
gnomAD - Genomes	Global	Study-wide	140038	A=0.217969	G=0.782031
gnomAD - Genomes	European	Sub	75850	A=0.25585	G=0.74415
gnomAD - Genomes	African	Sub	41962	A=0.12395	G=0.87605
gnomAD - Genomes	American	Sub	13632	A=0.30003	G=0.69997
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	A=0.2443	G=0.7557
gnomAD - Genomes	East Asian	Sub	3118	A=0.1507	G=0.8493
gnomAD - Genomes	Other	Sub	2152	A=0.2533	G=0.7467
14KJPN	JAPANESE	Study-wide	28258	A=0.14697	G=0.85303
Allele Frequency Aggregator	Total	Global	18890	A=0.23637	G=0.76363
Allele Frequency Aggregator	European	Sub	14286	A=0.25479	G=0.74521
Allele Frequency Aggregator	African	Sub	2946	A=0.1222	G=0.8778
Allele Frequency Aggregator	Other	Sub	692	A=0.218	G=0.782
Allele Frequency Aggregator	Latin American 2	Sub	610	A=0.398	G=0.602
Allele Frequency Aggregator	Latin American 1	Sub	146	A=0.260	G=0.740
Allele Frequency Aggregator	Asian	Sub	112	A=0.170	G=0.830
Allele Frequency Aggregator	South Asian	Sub	98	A=0.14	G=0.86
8.3KJPN	JAPANESE	Study-wide	16760	A=0.14356	G=0.85644
1000Genomes_30x	Global	Study-wide	6404	A=0.1818	G=0.8182
1000Genomes_30x	African	Sub	1786	A=0.0879	G=0.9121
1000Genomes_30x	Europe	Sub	1266	A=0.2607	G=0.7393
1000Genomes_30x	South Asian	Sub	1202	A=0.1373	G=0.8627
1000Genomes_30x	East Asian	Sub	1170	A=0.1462	G=0.8538
1000Genomes_30x	American	Sub	980	A=0.348	G=0.652
1000Genomes	Global	Study-wide	5008	A=0.1815	G=0.8185
1000Genomes	African	Sub	1322	A=0.0908	G=0.9092
1000Genomes	East Asian	Sub	1008	A=0.1468	G=0.8532
1000Genomes	Europe	Sub	1006	A=0.2594	G=0.7406
1000Genomes	South Asian	Sub	978	A=0.143	G=0.857
1000Genomes	American	Sub	694	A=0.346	G=0.654
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.2359	G=0.7641
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.2649	G=0.7351
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.2654	G=0.7346
KOREAN population from KRGDB	KOREAN	Study-wide	2930	A=0.1526	C=0.0000, G=0.8474
Korean Genome Project	KOREAN	Study-wide	1832	A=0.1605	G=0.8395
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.230	G=0.770
Northern Sweden	ACPOP	Study-wide	600	A=0.270	G=0.730
SGDP_PRJ	Global	Study-wide	532	A=0.158	G=0.842
Qatari	Global	Study-wide	216	A=0.245	G=0.755
A Vietnamese Genetic Variation Database	Global	Study-wide	212	A=0.203	G=0.797
Siberian	Global	Study-wide	54	A=0.17	G=0.83
The Danish reference pan genome	Danish	Study-wide	40	A=0.25	G=0.75

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 12	NC_000012.12:g.122600289A>C
GRCh38.p14 chr 12	NC_000012.12:g.122600289A>G
GRCh37.p13 chr 12	NC_000012.11:g.123084836A>C
GRCh37.p13 chr 12	NC_000012.11:g.123084836A>G
KNTC1 RefSeqGene	NG_046952.1:g.78041A>C
KNTC1 RefSeqGene	NG_046952.1:g.78041A>G

Gene: KNTC1, kinetochore associated 1 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
KNTC1 transcript	NM_014708.6:c.4564-1247A>C	N/A	Intron Variant
KNTC1 transcript variant X1	XM_006719706.3:c.4564-124… XM_006719706.3:c.4564-1247A>C	N/A	Intron Variant
KNTC1 transcript variant X2	XM_011539027.4:c.4564-124… XM_011539027.4:c.4564-1247A>C	N/A	Intron Variant
KNTC1 transcript variant X6	XM_011539029.4:c.4564-124… XM_011539029.4:c.4564-1247A>C	N/A	Intron Variant
KNTC1 transcript variant X3	XM_017020254.3:c.4564-228… XM_017020254.3:c.4564-2280A>C	N/A	Intron Variant
KNTC1 transcript variant X5	XM_017020255.3:c.4108-124… XM_017020255.3:c.4108-1247A>C	N/A	Intron Variant
KNTC1 transcript variant X10	XM_024449285.2:c.4356-228… XM_024449285.2:c.4356-2280A>C	N/A	Intron Variant
KNTC1 transcript variant X4	XM_047429917.1:c.4564-228… XM_047429917.1:c.4564-2280A>C	N/A	Intron Variant
KNTC1 transcript variant X9	XM_047429918.1:c.4356-124… XM_047429918.1:c.4356-1247A>C	N/A	Intron Variant
KNTC1 transcript variant X7	XM_011539030.1:c.	N/A	Genic Downstream Transcript Variant
KNTC1 transcript variant X8	XM_017020257.2:c.	N/A	Genic Downstream Transcript 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	A=	C	G
GRCh38.p14 chr 12	NC_000012.12:g.122600289=	NC_000012.12:g.122600289A>C	NC_000012.12:g.122600289A>G
GRCh37.p13 chr 12	NC_000012.11:g.123084836=	NC_000012.11:g.123084836A>C	NC_000012.11:g.123084836A>G
KNTC1 RefSeqGene	NG_046952.1:g.78041=	NG_046952.1:g.78041A>C	NG_046952.1:g.78041A>G
KNTC1 transcript	NM_014708.4:c.4564-1247=	NM_014708.4:c.4564-1247A>C	NM_014708.4:c.4564-1247A>G
KNTC1 transcript	NM_014708.6:c.4564-1247=	NM_014708.6:c.4564-1247A>C	NM_014708.6:c.4564-1247A>G
KNTC1 transcript variant X1	XM_005253654.1:c.2272-9095=	XM_005253654.1:c.2272-9095A>C	XM_005253654.1:c.2272-9095A>G
KNTC1 transcript variant X1	XM_006719706.3:c.4564-1247=	XM_006719706.3:c.4564-1247A>C	XM_006719706.3:c.4564-1247A>G
KNTC1 transcript variant X2	XM_011539027.4:c.4564-1247=	XM_011539027.4:c.4564-1247A>C	XM_011539027.4:c.4564-1247A>G
KNTC1 transcript variant X6	XM_011539029.4:c.4564-1247=	XM_011539029.4:c.4564-1247A>C	XM_011539029.4:c.4564-1247A>G
KNTC1 transcript variant X3	XM_017020254.3:c.4564-2280=	XM_017020254.3:c.4564-2280A>C	XM_017020254.3:c.4564-2280A>G
KNTC1 transcript variant X5	XM_017020255.3:c.4108-1247=	XM_017020255.3:c.4108-1247A>C	XM_017020255.3:c.4108-1247A>G
KNTC1 transcript variant X10	XM_024449285.2:c.4356-2280=	XM_024449285.2:c.4356-2280A>C	XM_024449285.2:c.4356-2280A>G
KNTC1 transcript variant X4	XM_047429917.1:c.4564-2280=	XM_047429917.1:c.4564-2280A>C	XM_047429917.1:c.4564-2280A>G
KNTC1 transcript variant X9	XM_047429918.1:c.4356-1247=	XM_047429918.1:c.4356-1247A>C	XM_047429918.1:c.4356-1247A>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#.

69 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss2973791	Apr 12, 2001 (94)
2	BCM_SSAHASNP	ss10708085	Jul 11, 2003 (116)
3	SC_SNP	ss15822861	Feb 27, 2004 (120)
4	SSAHASNP	ss20872324	Apr 05, 2004 (121)
5	ABI	ss40121983	Mar 14, 2006 (126)
6	HGSV	ss80128527	Dec 15, 2007 (130)
7	HGSV	ss83652210	Dec 15, 2007 (130)
8	BCMHGSC_JDW	ss89429911	Mar 24, 2008 (129)
9	HUMANGENOME_JCVI	ss97258598	Feb 05, 2009 (130)
10	COMPLETE_GENOMICS	ss168753585	Jul 04, 2010 (132)
11	COMPLETE_GENOMICS	ss171019774	Jul 04, 2010 (132)
12	BUSHMAN	ss198787743	Jul 04, 2010 (132)
13	BCM-HGSC-SUB	ss208424851	Jul 04, 2010 (132)
14	BL	ss255371677	May 09, 2011 (134)
15	GMI	ss281578126	May 04, 2012 (137)
16	GMI	ss286640059	Apr 25, 2013 (138)
17	PJP	ss291356008	May 09, 2011 (134)
18	1000GENOMES	ss337670529	May 09, 2011 (134)
19	TISHKOFF	ss563456578	Apr 25, 2013 (138)
20	SSMP	ss659042152	Apr 25, 2013 (138)
21	EVA-GONL	ss990044159	Aug 21, 2014 (142)
22	JMKIDD_LAB	ss1078832252	Aug 21, 2014 (142)
23	1000GENOMES	ss1346966773	Aug 21, 2014 (142)
24	DDI	ss1427078446	Apr 01, 2015 (144)
25	EVA_GENOME_DK	ss1576575159	Apr 01, 2015 (144)
26	EVA_UK10K_ALSPAC	ss1629620173	Apr 01, 2015 (144)
27	EVA_DECODE	ss1642154113	Apr 01, 2015 (144)
28	EVA_UK10K_TWINSUK	ss1672614206	Apr 01, 2015 (144)
29	HAMMER_LAB	ss1807456610	Sep 08, 2015 (146)
30	WEILL_CORNELL_DGM	ss1933399318	Feb 12, 2016 (147)
31	GENOMED	ss1967698256	Jul 19, 2016 (147)
32	JJLAB	ss2027455335	Sep 14, 2016 (149)
33	USC_VALOUEV	ss2155811694	Dec 20, 2016 (150)
34	HUMAN_LONGEVITY	ss2193876671	Dec 20, 2016 (150)
35	SYSTEMSBIOZJU	ss2628210991	Nov 08, 2017 (151)
36	GRF	ss2700171980	Nov 08, 2017 (151)
37	GNOMAD	ss2916118806	Nov 08, 2017 (151)
38	SWEGEN	ss3010485594	Nov 08, 2017 (151)
39	CSHL	ss3350287412	Nov 08, 2017 (151)
40	URBANLAB	ss3649938347	Oct 12, 2018 (152)
41	EGCUT_WGS	ss3677785891	Jul 13, 2019 (153)
42	EVA_DECODE	ss3694636605	Jul 13, 2019 (153)
43	ACPOP	ss3739454654	Jul 13, 2019 (153)
44	EVA	ss3751066813	Jul 13, 2019 (153)
45	PACBIO	ss3787358875	Jul 13, 2019 (153)
46	PACBIO	ss3792436964	Jul 13, 2019 (153)
47	PACBIO	ss3797320143	Jul 13, 2019 (153)
48	KHV_HUMAN_GENOMES	ss3816394916	Jul 13, 2019 (153)
49	EVA	ss3833369195	Apr 27, 2020 (154)
50	EVA	ss3840255138	Apr 27, 2020 (154)
51	EVA	ss3845744190	Apr 27, 2020 (154)
52	SGDP_PRJ	ss3879284340	Apr 27, 2020 (154)
53	KRGDB	ss3928060314	Apr 27, 2020 (154)
54	KOGIC	ss3972913599	Apr 27, 2020 (154)
55	TOPMED	ss4935594084	Apr 26, 2021 (155)
56	TOMMO_GENOMICS	ss5208556505	Apr 26, 2021 (155)
57	1000G_HIGH_COVERAGE	ss5292529252	Oct 16, 2022 (156)
58	EVA	ss5408760363	Oct 16, 2022 (156)
59	HUGCELL_USP	ss5487103422	Oct 16, 2022 (156)
60	EVA	ss5510868404	Oct 16, 2022 (156)
61	1000G_HIGH_COVERAGE	ss5590890066	Oct 16, 2022 (156)
62	SANFORD_IMAGENETICS	ss5654118358	Oct 16, 2022 (156)
63	TOMMO_GENOMICS	ss5759002726	Oct 16, 2022 (156)
64	YY_MCH	ss5813718016	Oct 16, 2022 (156)
65	EVA	ss5838628063	Oct 16, 2022 (156)
66	EVA	ss5850583343	Oct 16, 2022 (156)
67	EVA	ss5906356181	Oct 16, 2022 (156)
68	EVA	ss5945532565	Oct 16, 2022 (156)
69	EVA	ss5980767177	Oct 16, 2022 (156)
70	1000Genomes	NC_000012.11 - 123084836	Oct 12, 2018 (152)
71	1000Genomes_30x	NC_000012.12 - 122600289	Oct 16, 2022 (156)
72	The Avon Longitudinal Study of Parents and Children	NC_000012.11 - 123084836	Oct 12, 2018 (152)
73	Genetic variation in the Estonian population	NC_000012.11 - 123084836	Oct 12, 2018 (152)
74	The Danish reference pan genome	NC_000012.11 - 123084836	Apr 27, 2020 (154)
75	gnomAD - Genomes	NC_000012.12 - 122600289	Apr 26, 2021 (155)
76	Genome of the Netherlands Release 5	NC_000012.11 - 123084836	Apr 27, 2020 (154)
77	KOREAN population from KRGDB	NC_000012.11 - 123084836	Apr 27, 2020 (154)
78	Korean Genome Project	NC_000012.12 - 122600289	Apr 27, 2020 (154)
79	Northern Sweden	NC_000012.11 - 123084836	Jul 13, 2019 (153)
80	Qatari	NC_000012.11 - 123084836	Apr 27, 2020 (154)
81	SGDP_PRJ	NC_000012.11 - 123084836	Apr 27, 2020 (154)
82	Siberian	NC_000012.11 - 123084836	Apr 27, 2020 (154)
83	8.3KJPN	NC_000012.11 - 123084836	Apr 26, 2021 (155)
84	14KJPN	NC_000012.12 - 122600289	Oct 16, 2022 (156)
85	TopMed	NC_000012.12 - 122600289	Apr 26, 2021 (155)
86	UK 10K study - Twins	NC_000012.11 - 123084836	Oct 12, 2018 (152)
87	A Vietnamese Genetic Variation Database	NC_000012.11 - 123084836	Jul 13, 2019 (153)
88	ALFA	NC_000012.12 - 122600289	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)
rs59187353	May 25, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
35237708, ss3928060314	NC_000012.11:123084835:A:C	NC_000012.12:122600288:A:C	(self)
ss80128527, ss83652210	NC_000012.9:121609715:A:G	NC_000012.12:122600288:A:G	(self)
ss89429911, ss168753585, ss171019774, ss198787743, ss208424851, ss255371677, ss281578126, ss286640059, ss291356008, ss1642154113	NC_000012.10:121650788:A:G	NC_000012.12:122600288:A:G	(self)
59790081, 33209851, 23524139, 3159551, 14809497, 35237708, 12739519, 15441248, 31301320, 8328048, 66525812, 33209851, 7365630, ss337670529, ss563456578, ss659042152, ss990044159, ss1078832252, ss1346966773, ss1427078446, ss1576575159, ss1629620173, ss1672614206, ss1807456610, ss1933399318, ss1967698256, ss2027455335, ss2155811694, ss2628210991, ss2700171980, ss2916118806, ss3010485594, ss3350287412, ss3677785891, ss3739454654, ss3751066813, ss3787358875, ss3792436964, ss3797320143, ss3833369195, ss3840255138, ss3879284340, ss3928060314, ss5208556505, ss5408760363, ss5510868404, ss5654118358, ss5838628063, ss5945532565, ss5980767177	NC_000012.11:123084835:A:G	NC_000012.12:122600288:A:G	(self)
78416001, 421747562, 29291600, 92839830, 151139741, 13774411870, ss2193876671, ss3649938347, ss3694636605, ss3816394916, ss3845744190, ss3972913599, ss4935594084, ss5292529252, ss5487103422, ss5590890066, ss5759002726, ss5813718016, ss5850583343, ss5906356181	NC_000012.12:122600288:A:G	NC_000012.12:122600288:A:G	(self)
ss10708085	NT_009755.15:478415:A:G	NC_000012.12:122600288:A:G	(self)
ss15822861, ss20872324	NT_009755.16:478415:A:G	NC_000012.12:122600288:A:G	(self)
ss2973791, ss40121983, ss97258598	NT_009755.19:504212:A:G	NC_000012.12:122600288:A:G	(self)

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

No publications for rs2062506

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs2062506