Name: rs6062293
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.

rs6062293

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr20:63645516 (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: C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.442453 (117113/264690, TOPMED)
T=0.457393 (64013/139952, GnomAD)
T=0.48578 (17120/35242, ALFA) (+ 15 more)
T=0.09293 (2626/28258, 14KJPN)
T=0.09135 (1531/16760, 8.3KJPN)
T=0.3485 (2232/6404, 1000G_30x)
T=0.3425 (1715/5008, 1000G)
C=0.4871 (2182/4480, Estonian)
T=0.4943 (1905/3854, ALSPAC)
T=0.4660 (1728/3708, TWINSUK)
T=0.0927 (271/2922, KOREAN)
T=0.471 (470/998, GoNL)
T=0.472 (283/600, NorthernSweden)
C=0.353 (103/292, SGDP_PRJ)
T=0.472 (102/216, Qatari)
T=0.084 (18/214, Vietnamese)
T=0.47 (19/40, GENOME_DK)
C=0.42 (11/26, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: STMN3 : 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	35242	C=0.51422	T=0.48578
European	Sub	30366	C=0.50175	T=0.49825
African	Sub	2946	C=0.5821	T=0.4179
African Others	Sub	114	C=0.570	T=0.430
African American	Sub	2832	C=0.5826	T=0.4174
Asian	Sub	156	C=0.878	T=0.122
East Asian	Sub	130	C=0.862	T=0.138
Other Asian	Sub	26	C=0.96	T=0.04
Latin American 1	Sub	146	C=0.466	T=0.534
Latin American 2	Sub	610	C=0.611	T=0.389
South Asian	Sub	98	C=0.66	T=0.34
Other	Sub	920	C=0.574	T=0.426

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	C=0.557547	T=0.442453
gnomAD - Genomes	Global	Study-wide	139952	C=0.542607	T=0.457393
gnomAD - Genomes	European	Sub	75848	C=0.50724	T=0.49276
gnomAD - Genomes	African	Sub	41898	C=0.58203	T=0.41797
gnomAD - Genomes	American	Sub	13608	C=0.55644	T=0.44356
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	C=0.4774	T=0.5226
gnomAD - Genomes	East Asian	Sub	3126	C=0.8756	T=0.1244
gnomAD - Genomes	Other	Sub	2148	C=0.5512	T=0.4488
Allele Frequency Aggregator	Total	Global	35242	C=0.51422	T=0.48578
Allele Frequency Aggregator	European	Sub	30366	C=0.50175	T=0.49825
Allele Frequency Aggregator	African	Sub	2946	C=0.5821	T=0.4179
Allele Frequency Aggregator	Other	Sub	920	C=0.574	T=0.426
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.611	T=0.389
Allele Frequency Aggregator	Asian	Sub	156	C=0.878	T=0.122
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.466	T=0.534
Allele Frequency Aggregator	South Asian	Sub	98	C=0.66	T=0.34
14KJPN	JAPANESE	Study-wide	28258	C=0.90707	T=0.09293
8.3KJPN	JAPANESE	Study-wide	16760	C=0.90865	T=0.09135
1000Genomes_30x	Global	Study-wide	6404	C=0.6515	T=0.3485
1000Genomes_30x	African	Sub	1786	C=0.5745	T=0.4255
1000Genomes_30x	Europe	Sub	1266	C=0.5024	T=0.4976
1000Genomes_30x	South Asian	Sub	1202	C=0.7321	T=0.2679
1000Genomes_30x	East Asian	Sub	1170	C=0.9043	T=0.0957
1000Genomes_30x	American	Sub	980	C=0.584	T=0.416
1000Genomes	Global	Study-wide	5008	C=0.6575	T=0.3425
1000Genomes	African	Sub	1322	C=0.5794	T=0.4206
1000Genomes	East Asian	Sub	1008	C=0.9018	T=0.0982
1000Genomes	Europe	Sub	1006	C=0.5010	T=0.4990
1000Genomes	South Asian	Sub	978	C=0.733	T=0.267
1000Genomes	American	Sub	694	C=0.572	T=0.428
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.4871	T=0.5129
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.5057	T=0.4943
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.5340	T=0.4660
KOREAN population from KRGDB	KOREAN	Study-wide	2922	C=0.9073	T=0.0927
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.529	T=0.471
Northern Sweden	ACPOP	Study-wide	600	C=0.528	T=0.472
SGDP_PRJ	Global	Study-wide	292	C=0.353	T=0.647
Qatari	Global	Study-wide	216	C=0.528	T=0.472
A Vietnamese Genetic Variation Database	Global	Study-wide	214	C=0.916	T=0.084
The Danish reference pan genome	Danish	Study-wide	40	C=0.53	T=0.47
Siberian	Global	Study-wide	26	C=0.42	T=0.58

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 20	NC_000020.11:g.63645516C>T
GRCh37.p13 chr 20	NC_000020.10:g.62276869C>T

Gene: STMN3, stathmin 3 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
STMN3 transcript variant 2	NM_001276310.2:c.-14-1207… NM_001276310.2:c.-14-1207G>A	N/A	Intron Variant
STMN3 transcript variant 1	NM_015894.4:c.20-1207G>A	N/A	Intron Variant
STMN3 transcript variant 3	NR_075070.2:n.	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	C=	T
GRCh38.p14 chr 20	NC_000020.11:g.63645516=	NC_000020.11:g.63645516C>T
GRCh37.p13 chr 20	NC_000020.10:g.62276869=	NC_000020.10:g.62276869C>T
STMN3 transcript variant 2	NM_001276310.1:c.-14-1207=	NM_001276310.1:c.-14-1207G>A
STMN3 transcript variant 2	NM_001276310.2:c.-14-1207=	NM_001276310.2:c.-14-1207G>A
STMN3 transcript variant 1	NM_015894.3:c.20-1207=	NM_015894.3:c.20-1207G>A
STMN3 transcript variant 1	NM_015894.4:c.20-1207=	NM_015894.4:c.20-1207G>A

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#.

67 SubSNP, 18 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss8377814	Apr 21, 2003 (114)
2	BCM_SSAHASNP	ss10958077	Jul 11, 2003 (117)
3	BCMHGSC_JDW	ss91756691	Mar 24, 2008 (129)
4	1000GENOMES	ss112248327	Jan 25, 2009 (130)
5	1000GENOMES	ss113573872	Jan 25, 2009 (130)
6	ENSEMBL	ss138272504	Dec 01, 2009 (131)
7	COMPLETE_GENOMICS	ss168433528	Jul 04, 2010 (132)
8	COMPLETE_GENOMICS	ss170106933	Jul 04, 2010 (132)
9	COMPLETE_GENOMICS	ss172211162	Jul 04, 2010 (132)
10	BUSHMAN	ss203946733	Jul 04, 2010 (132)
11	1000GENOMES	ss228452532	Jul 14, 2010 (132)
12	1000GENOMES	ss237902316	Jul 15, 2010 (132)
13	1000GENOMES	ss244057750	Jul 15, 2010 (132)
14	GMI	ss283446442	May 04, 2012 (137)
15	PJP	ss292599580	May 09, 2011 (134)
16	TISHKOFF	ss566368733	Apr 25, 2013 (138)
17	SSMP	ss662250039	Apr 25, 2013 (138)
18	EVA-GONL	ss994910091	Aug 21, 2014 (142)
19	JMKIDD_LAB	ss1082340005	Aug 21, 2014 (142)
20	1000GENOMES	ss1365495752	Aug 21, 2014 (142)
21	DDI	ss1429106983	Apr 01, 2015 (144)
22	EVA_GENOME_DK	ss1579578480	Apr 01, 2015 (144)
23	EVA_UK10K_ALSPAC	ss1639167758	Apr 01, 2015 (144)
24	EVA_UK10K_TWINSUK	ss1682161791	Apr 01, 2015 (144)
25	EVA_DECODE	ss1698974884	Apr 01, 2015 (144)
26	HAMMER_LAB	ss1809586307	Sep 08, 2015 (146)
27	WEILL_CORNELL_DGM	ss1938433424	Feb 12, 2016 (147)
28	GENOMED	ss1969172339	Jul 19, 2016 (147)
29	JJLAB	ss2029996992	Sep 14, 2016 (149)
30	ILLUMINA	ss2094920266	Dec 20, 2016 (150)
31	ILLUMINA	ss2095117269	Dec 20, 2016 (150)
32	USC_VALOUEV	ss2158569031	Dec 20, 2016 (150)
33	HUMAN_LONGEVITY	ss2244247584	Dec 20, 2016 (150)
34	GRF	ss2704266564	Nov 08, 2017 (151)
35	ILLUMINA	ss2710945291	Nov 08, 2017 (151)
36	GNOMAD	ss2969446233	Nov 08, 2017 (151)
37	SWEGEN	ss3018477977	Nov 08, 2017 (151)
38	BIOINF_KMB_FNS_UNIBA	ss3028831876	Nov 08, 2017 (151)
39	CSHL	ss3352597384	Nov 08, 2017 (151)
40	ILLUMINA	ss3652596822	Oct 12, 2018 (152)
41	EGCUT_WGS	ss3685163076	Jul 13, 2019 (153)
42	EVA_DECODE	ss3707316936	Jul 13, 2019 (153)
43	ACPOP	ss3743553893	Jul 13, 2019 (153)
44	EVA	ss3758871353	Jul 13, 2019 (153)
45	PACBIO	ss3788696200	Jul 13, 2019 (153)
46	PACBIO	ss3793580094	Jul 13, 2019 (153)
47	PACBIO	ss3798467554	Jul 13, 2019 (153)
48	KHV_HUMAN_GENOMES	ss3822024856	Jul 13, 2019 (153)
49	EVA	ss3835766037	Apr 27, 2020 (154)
50	EVA	ss3841507935	Apr 27, 2020 (154)
51	EVA	ss3847021759	Apr 27, 2020 (154)
52	SGDP_PRJ	ss3889491148	Apr 27, 2020 (154)
53	KRGDB	ss3939818777	Apr 27, 2020 (154)
54	TOPMED	ss5094751112	Apr 27, 2021 (155)
55	TOMMO_GENOMICS	ss5230476325	Apr 27, 2021 (155)
56	1000G_HIGH_COVERAGE	ss5309443341	Oct 16, 2022 (156)
57	EVA	ss5438584601	Oct 16, 2022 (156)
58	HUGCELL_USP	ss5501658047	Oct 16, 2022 (156)
59	1000G_HIGH_COVERAGE	ss5616201686	Oct 16, 2022 (156)
60	SANFORD_IMAGENETICS	ss5663572564	Oct 16, 2022 (156)
61	TOMMO_GENOMICS	ss5790542988	Oct 16, 2022 (156)
62	YY_MCH	ss5818201721	Oct 16, 2022 (156)
63	EVA	ss5845947490	Oct 16, 2022 (156)
64	EVA	ss5853217725	Oct 16, 2022 (156)
65	EVA	ss5924167379	Oct 16, 2022 (156)
66	EVA	ss5958505805	Oct 16, 2022 (156)
67	EVA	ss5981099908	Oct 16, 2022 (156)
68	1000Genomes	NC_000020.10 - 62276869	Oct 12, 2018 (152)
69	1000Genomes_30x	NC_000020.11 - 63645516	Oct 16, 2022 (156)
70	The Avon Longitudinal Study of Parents and Children	NC_000020.10 - 62276869	Oct 12, 2018 (152)
71	Genetic variation in the Estonian population	NC_000020.10 - 62276869	Oct 12, 2018 (152)
72	The Danish reference pan genome	NC_000020.10 - 62276869	Apr 27, 2020 (154)
73	gnomAD - Genomes	NC_000020.11 - 63645516	Apr 27, 2021 (155)
74	Genome of the Netherlands Release 5	NC_000020.10 - 62276869	Apr 27, 2020 (154)
75	KOREAN population from KRGDB	NC_000020.10 - 62276869	Apr 27, 2020 (154)
76	Northern Sweden	NC_000020.10 - 62276869	Jul 13, 2019 (153)
77	Qatari	NC_000020.10 - 62276869	Apr 27, 2020 (154)
78	SGDP_PRJ	NC_000020.10 - 62276869	Apr 27, 2020 (154)
79	Siberian	NC_000020.10 - 62276869	Apr 27, 2020 (154)
80	8.3KJPN	NC_000020.10 - 62276869	Apr 27, 2021 (155)
81	14KJPN	NC_000020.11 - 63645516	Oct 16, 2022 (156)
82	TopMed	NC_000020.11 - 63645516	Apr 27, 2021 (155)
83	UK 10K study - Twins	NC_000020.10 - 62276869	Oct 12, 2018 (152)
84	A Vietnamese Genetic Variation Database	NC_000020.10 - 62276869	Jul 13, 2019 (153)
85	ALFA	NC_000020.11 - 63645516	Apr 27, 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)
rs7267231	Aug 26, 2003 (117)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss91756691, ss112248327, ss113573872, ss168433528, ss170106933, ss172211162, ss203946733, ss283446442, ss292599580, ss1698974884, ss2094920266	NC_000020.9:61747312:C:T	NC_000020.11:63645515:C:T	(self)
78984099, 43733256, 30901324, 5743419, 19475534, 46996171, 16838758, 20475346, 41508128, 11085385, 88445632, 43733256, 9643617, ss228452532, ss237902316, ss244057750, ss566368733, ss662250039, ss994910091, ss1082340005, ss1365495752, ss1429106983, ss1579578480, ss1639167758, ss1682161791, ss1809586307, ss1938433424, ss1969172339, ss2029996992, ss2095117269, ss2158569031, ss2704266564, ss2710945291, ss2969446233, ss3018477977, ss3352597384, ss3652596822, ss3685163076, ss3743553893, ss3758871353, ss3788696200, ss3793580094, ss3798467554, ss3835766037, ss3841507935, ss3889491148, ss3939818777, ss5230476325, ss5438584601, ss5663572564, ss5845947490, ss5958505805, ss5981099908	NC_000020.10:62276868:C:T	NC_000020.11:63645515:C:T	(self)
103727621, 557006592, 124380092, 369860057, 12814460509, ss2244247584, ss3028831876, ss3707316936, ss3822024856, ss3847021759, ss5094751112, ss5309443341, ss5501658047, ss5616201686, ss5790542988, ss5818201721, ss5853217725, ss5924167379	NC_000020.11:63645515:C:T	NC_000020.11:63645515:C:T	(self)
ss8377814, ss10958077	NT_011333.5:1013498:C:T	NC_000020.11:63645515:C:T	(self)
ss138272504	NT_011333.6:1013499:C:T	NC_000020.11:63645515:C:T	(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 rs6062293

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

rs6062293