Name: rs6037425
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.

rs6037425

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr20:2856733 (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>A / C>G / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.459334 (121581/264690, TOPMED)
C=0.484025 (67777/140028, GnomAD)
C=0.33707 (9525/28258, 14KJPN) (+ 16 more)
G=0.43928 (8298/18890, ALFA)
C=0.33813 (5667/16760, 8.3KJPN)
C=0.3923 (2512/6404, 1000G_30x)
C=0.3986 (1996/5008, 1000G)
G=0.3616 (1620/4480, Estonian)
G=0.3646 (1405/3854, ALSPAC)
G=0.3681 (1365/3708, TWINSUK)
C=0.2966 (869/2930, KOREAN)
C=0.3701 (698/1886, HapMap)
G=0.364 (363/998, GoNL)
G=0.393 (236/600, NorthernSweden)
C=0.265 (109/412, SGDP_PRJ)
G=0.412 (89/216, Qatari)
G=0.477 (103/216, Vietnamese)
C=0.31 (13/42, Siberian)
G=0.35 (14/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: VPS16 : 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	C=0.56072	G=0.43928
European	Sub	14286	C=0.64560	G=0.35440
African	Sub	2946	C=0.2128	G=0.7872
African Others	Sub	114	C=0.167	G=0.833
African American	Sub	2832	C=0.2147	G=0.7853
Asian	Sub	112	C=0.464	G=0.536
East Asian	Sub	86	C=0.40	G=0.60
Other Asian	Sub	26	C=0.69	G=0.31
Latin American 1	Sub	146	C=0.459	G=0.541
Latin American 2	Sub	610	C=0.374	G=0.626
South Asian	Sub	98	C=0.51	G=0.49
Other	Sub	692	C=0.499	G=0.501

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=0.459334	G=0.540666
gnomAD - Genomes	Global	Study-wide	140028	C=0.484025	G=0.515975
gnomAD - Genomes	European	Sub	75816	C=0.63404	G=0.36596
gnomAD - Genomes	African	Sub	42000	C=0.21745	G=0.78255
gnomAD - Genomes	American	Sub	13628	C=0.44064	G=0.55936
gnomAD - Genomes	Ashkenazi Jewish	Sub	3316	C=0.6963	G=0.3037
gnomAD - Genomes	East Asian	Sub	3118	C=0.4118	G=0.5882
gnomAD - Genomes	Other	Sub	2150	C=0.4540	G=0.5460
14KJPN	JAPANESE	Study-wide	28258	C=0.33707	G=0.66293
Allele Frequency Aggregator	Total	Global	18890	C=0.56072	G=0.43928
Allele Frequency Aggregator	European	Sub	14286	C=0.64560	G=0.35440
Allele Frequency Aggregator	African	Sub	2946	C=0.2128	G=0.7872
Allele Frequency Aggregator	Other	Sub	692	C=0.499	G=0.501
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.374	G=0.626
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.459	G=0.541
Allele Frequency Aggregator	Asian	Sub	112	C=0.464	G=0.536
Allele Frequency Aggregator	South Asian	Sub	98	C=0.51	G=0.49
8.3KJPN	JAPANESE	Study-wide	16760	C=0.33813	G=0.66187
1000Genomes_30x	Global	Study-wide	6404	C=0.3923	G=0.6077
1000Genomes_30x	African	Sub	1786	C=0.1310	G=0.8690
1000Genomes_30x	Europe	Sub	1266	C=0.6398	G=0.3602
1000Genomes_30x	South Asian	Sub	1202	C=0.5133	G=0.4867
1000Genomes_30x	East Asian	Sub	1170	C=0.4231	G=0.5769
1000Genomes_30x	American	Sub	980	C=0.363	G=0.637
1000Genomes	Global	Study-wide	5008	C=0.3986	G=0.6014
1000Genomes	African	Sub	1322	C=0.1309	G=0.8691
1000Genomes	East Asian	Sub	1008	C=0.4246	G=0.5754
1000Genomes	Europe	Sub	1006	C=0.6461	G=0.3539
1000Genomes	South Asian	Sub	978	C=0.505	G=0.495
1000Genomes	American	Sub	694	C=0.362	G=0.638
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.6384	G=0.3616
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.6354	G=0.3646
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.6319	G=0.3681
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.2966	A=0.0000, G=0.7034, T=0.0000
HapMap	Global	Study-wide	1886	C=0.3701	G=0.6299
HapMap	American	Sub	768	C=0.495	G=0.505
HapMap	African	Sub	688	C=0.157	G=0.843
HapMap	Asian	Sub	254	C=0.350	G=0.650
HapMap	Europe	Sub	176	C=0.688	G=0.312
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.636	G=0.364
Northern Sweden	ACPOP	Study-wide	600	C=0.607	G=0.393
SGDP_PRJ	Global	Study-wide	412	C=0.265	G=0.735
Qatari	Global	Study-wide	216	C=0.588	G=0.412
A Vietnamese Genetic Variation Database	Global	Study-wide	216	C=0.523	G=0.477
Siberian	Global	Study-wide	42	C=0.31	G=0.69
The Danish reference pan genome	Danish	Study-wide	40	C=0.65	G=0.35

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.2856733C>A
GRCh38.p14 chr 20	NC_000020.11:g.2856733C>G
GRCh38.p14 chr 20	NC_000020.11:g.2856733C>T
GRCh37.p13 chr 20	NC_000020.10:g.2837379C>A
GRCh37.p13 chr 20	NC_000020.10:g.2837379C>G
GRCh37.p13 chr 20	NC_000020.10:g.2837379C>T

Gene: VPS16, VPS16 core subunit of CORVET and HOPS complexes (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
VPS16 transcript variant 1	NM_022575.4:c.54-2986C>A	N/A	Intron Variant
VPS16 transcript variant 3	NM_080413.3:c.54-2986C>A	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=	A	G	T
GRCh38.p14 chr 20	NC_000020.11:g.2856733=	NC_000020.11:g.2856733C>A	NC_000020.11:g.2856733C>G	NC_000020.11:g.2856733C>T
GRCh37.p13 chr 20	NC_000020.10:g.2837379=	NC_000020.10:g.2837379C>A	NC_000020.10:g.2837379C>G	NC_000020.10:g.2837379C>T
VPS16 transcript variant 1	NM_022575.2:c.54-2986=	NM_022575.2:c.54-2986C>A	NM_022575.2:c.54-2986C>G	NM_022575.2:c.54-2986C>T
VPS16 transcript variant 1	NM_022575.4:c.54-2986=	NM_022575.4:c.54-2986C>A	NM_022575.4:c.54-2986C>G	NM_022575.4:c.54-2986C>T
VPS16 transcript variant 3	NM_080413.1:c.54-2986=	NM_080413.1:c.54-2986C>A	NM_080413.1:c.54-2986C>G	NM_080413.1:c.54-2986C>T
VPS16 transcript variant 3	NM_080413.3:c.54-2986=	NM_080413.3:c.54-2986C>A	NM_080413.3:c.54-2986C>G	NM_080413.3:c.54-2986C>T

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#.

81 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss8345191	Apr 21, 2003 (114)
2	WI_SSAHASNP	ss12488410	Jul 11, 2003 (117)
3	CSHL-HAPMAP	ss19476669	Feb 27, 2004 (120)
4	SSAHASNP	ss21765785	Apr 05, 2004 (121)
5	PERLEGEN	ss24069293	Sep 20, 2004 (123)
6	ABI	ss44229482	Mar 13, 2006 (126)
7	CSHL-HAPMAP	ss68421366	Jan 12, 2007 (127)
8	AFFY	ss76848392	Dec 08, 2007 (130)
9	HGSV	ss82280181	Dec 15, 2007 (130)
10	HGSV	ss84722138	Dec 15, 2007 (130)
11	BCMHGSC_JDW	ss91618656	Mar 24, 2008 (129)
12	HUMANGENOME_JCVI	ss96209444	Feb 06, 2009 (130)
13	BGI	ss103716023	Dec 01, 2009 (131)
14	KRIBB_YJKIM	ss104918662	Feb 06, 2009 (130)
15	1000GENOMES	ss111622937	Jan 25, 2009 (130)
16	1000GENOMES	ss115377747	Jan 25, 2009 (130)
17	ILLUMINA-UK	ss117461438	Feb 14, 2009 (130)
18	ENSEMBL	ss135731997	Dec 01, 2009 (131)
19	ENSEMBL	ss138200241	Dec 01, 2009 (131)
20	GMI	ss156090365	Dec 01, 2009 (131)
21	COMPLETE_GENOMICS	ss167685697	Jul 04, 2010 (132)
22	COMPLETE_GENOMICS	ss168899919	Jul 04, 2010 (132)
23	COMPLETE_GENOMICS	ss171831571	Jul 04, 2010 (132)
24	BUSHMAN	ss203811656	Jul 04, 2010 (132)
25	BCM-HGSC-SUB	ss208715856	Jul 04, 2010 (132)
26	1000GENOMES	ss228223699	Jul 14, 2010 (132)
27	1000GENOMES	ss237739260	Jul 15, 2010 (132)
28	1000GENOMES	ss243930723	Jul 15, 2010 (132)
29	GMI	ss283277643	May 04, 2012 (137)
30	PJP	ss292565278	May 09, 2011 (134)
31	TISHKOFF	ss566098130	Apr 25, 2013 (138)
32	SSMP	ss661967720	Apr 25, 2013 (138)
33	EVA-GONL	ss994479857	Aug 21, 2014 (142)
34	JMKIDD_LAB	ss1082026873	Aug 21, 2014 (142)
35	1000GENOMES	ss1363848161	Aug 21, 2014 (142)
36	DDI	ss1428978142	Apr 01, 2015 (144)
37	EVA_GENOME_DK	ss1579412210	Apr 01, 2015 (144)
38	EVA_UK10K_ALSPAC	ss1638294807	Apr 01, 2015 (144)
39	EVA_UK10K_TWINSUK	ss1681288840	Apr 01, 2015 (144)
40	EVA_DECODE	ss1698534096	Apr 01, 2015 (144)
41	EVA_SVP	ss1713674518	Apr 01, 2015 (144)
42	HAMMER_LAB	ss1809395178	Sep 08, 2015 (146)
43	WEILL_CORNELL_DGM	ss1937988906	Feb 12, 2016 (147)
44	GENOMED	ss1969076639	Jul 19, 2016 (147)
45	JJLAB	ss2029771123	Sep 14, 2016 (149)
46	USC_VALOUEV	ss2158324988	Dec 20, 2016 (150)
47	HUMAN_LONGEVITY	ss2240879568	Dec 20, 2016 (150)
48	SYSTEMSBIOZJU	ss2629383161	Nov 08, 2017 (151)
49	GRF	ss2703996580	Nov 08, 2017 (151)
50	GNOMAD	ss2964827588	Nov 08, 2017 (151)
51	SWEGEN	ss3017778149	Nov 08, 2017 (151)
52	BIOINF_KMB_FNS_UNIBA	ss3028717556	Nov 08, 2017 (151)
53	CSHL	ss3352391276	Nov 08, 2017 (151)
54	URBANLAB	ss3650958239	Oct 12, 2018 (152)
55	EGCUT_WGS	ss3684491844	Jul 13, 2019 (153)
56	EVA_DECODE	ss3706448338	Jul 13, 2019 (153)
57	ACPOP	ss3743198801	Jul 13, 2019 (153)
58	EVA	ss3758353655	Jul 13, 2019 (153)
59	PACBIO	ss3788583737	Jul 13, 2019 (153)
60	PACBIO	ss3793486328	Jul 13, 2019 (153)
61	PACBIO	ss3798373458	Jul 13, 2019 (153)
62	KHV_HUMAN_GENOMES	ss3821525470	Jul 13, 2019 (153)
63	EVA	ss3835557246	Apr 27, 2020 (154)
64	EVA	ss3841402284	Apr 27, 2020 (154)
65	EVA	ss3846909686	Apr 27, 2020 (154)
66	SGDP_PRJ	ss3888615989	Apr 27, 2020 (154)
67	KRGDB	ss3938795035	Apr 27, 2020 (154)
68	TOPMED	ss5080416512	Apr 27, 2021 (155)
69	TOMMO_GENOMICS	ss5228597132	Apr 27, 2021 (155)
70	1000G_HIGH_COVERAGE	ss5307893443	Oct 16, 2022 (156)
71	EVA	ss5435912032	Oct 16, 2022 (156)
72	HUGCELL_USP	ss5500312983	Oct 16, 2022 (156)
73	EVA	ss5512139357	Oct 16, 2022 (156)
74	1000G_HIGH_COVERAGE	ss5613882591	Oct 16, 2022 (156)
75	SANFORD_IMAGENETICS	ss5662753776	Oct 16, 2022 (156)
76	TOMMO_GENOMICS	ss5787515563	Oct 16, 2022 (156)
77	YY_MCH	ss5817767303	Oct 16, 2022 (156)
78	EVA	ss5845367019	Oct 16, 2022 (156)
79	EVA	ss5853043926	Oct 16, 2022 (156)
80	EVA	ss5922455362	Oct 16, 2022 (156)
81	EVA	ss5957651721	Oct 16, 2022 (156)
82	1000Genomes	NC_000020.10 - 2837379	Oct 12, 2018 (152)
83	1000Genomes_30x	NC_000020.11 - 2856733	Oct 16, 2022 (156)
84	The Avon Longitudinal Study of Parents and Children	NC_000020.10 - 2837379	Oct 12, 2018 (152)
85	Genetic variation in the Estonian population	NC_000020.10 - 2837379	Oct 12, 2018 (152)
86	The Danish reference pan genome	NC_000020.10 - 2837379	Apr 27, 2020 (154)
87	gnomAD - Genomes	NC_000020.11 - 2856733	Apr 27, 2021 (155)
88	Genome of the Netherlands Release 5	NC_000020.10 - 2837379	Apr 27, 2020 (154)
89	HapMap	NC_000020.11 - 2856733	Apr 27, 2020 (154)
90	KOREAN population from KRGDB	NC_000020.10 - 2837379	Apr 27, 2020 (154)
91	Northern Sweden	NC_000020.10 - 2837379	Jul 13, 2019 (153)
92	Qatari	NC_000020.10 - 2837379	Apr 27, 2020 (154)
93	SGDP_PRJ	NC_000020.10 - 2837379	Apr 27, 2020 (154)
94	Siberian	NC_000020.10 - 2837379	Apr 27, 2020 (154)
95	8.3KJPN	NC_000020.10 - 2837379	Apr 27, 2021 (155)
96	14KJPN	NC_000020.11 - 2856733	Oct 16, 2022 (156)
97	TopMed	NC_000020.11 - 2856733	Apr 27, 2021 (155)
98	UK 10K study - Twins	NC_000020.10 - 2837379	Oct 12, 2018 (152)
99	A Vietnamese Genetic Variation Database	NC_000020.10 - 2837379	Jul 13, 2019 (153)
100	ALFA	NC_000020.11 - 2856733	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)
rs8120817	Aug 26, 2003 (117)
rs16988136	Oct 07, 2004 (123)
rs56474927	May 25, 2008 (130)
rs60262756	May 25, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
45972429, ss3938795035	NC_000020.10:2837378:C:A	NC_000020.11:2856732:C:A	(self)
ss76848392, ss82280181, ss84722138, ss91618656, ss111622937, ss115377747, ss117461438, ss167685697, ss168899919, ss171831571, ss203811656, ss208715856, ss283277643, ss292565278, ss1698534096, ss1713674518	NC_000020.9:2785378:C:G	NC_000020.11:2856732:C:G	(self)
77279912, 42775711, 30230092, 5577149, 19059747, 45972429, 16483666, 20030828, 40632969, 10841342, 86566439, 42775711, 9443029, ss228223699, ss237739260, ss243930723, ss566098130, ss661967720, ss994479857, ss1082026873, ss1363848161, ss1428978142, ss1579412210, ss1638294807, ss1681288840, ss1809395178, ss1937988906, ss1969076639, ss2029771123, ss2158324988, ss2629383161, ss2703996580, ss2964827588, ss3017778149, ss3352391276, ss3684491844, ss3743198801, ss3758353655, ss3788583737, ss3793486328, ss3798373458, ss3835557246, ss3841402284, ss3888615989, ss3938795035, ss5228597132, ss5435912032, ss5512139357, ss5662753776, ss5845367019, ss5957651721	NC_000020.10:2837378:C:G	NC_000020.11:2856732:C:G	(self)
101408526, 544947751, 2053791, 121352667, 355525457, 16091175949, ss2240879568, ss3028717556, ss3650958239, ss3706448338, ss3821525470, ss3846909686, ss5080416512, ss5307893443, ss5500312983, ss5613882591, ss5787515563, ss5817767303, ss5853043926, ss5922455362	NC_000020.11:2856732:C:G	NC_000020.11:2856732:C:G	(self)
ss8345191, ss12488410, ss19476669, ss21765785, ss24069293, ss44229482, ss68421366, ss96209444, ss103716023, ss104918662, ss135731997, ss138200241, ss156090365	NT_011387.8:2777378:C:G	NC_000020.11:2856732:C:G	(self)
45972429, ss3938795035	NC_000020.10:2837378:C:T	NC_000020.11:2856732: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 rs6037425

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

rs6037425