Name: rs6422639
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.

rs6422639

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:217188277 (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>G
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.243681 (64500/264690, TOPMED)
A=0.247143 (34555/139818, GnomAD)
A=0.07574 (2140/28256, 14KJPN) (+ 16 more)
A=0.27401 (5176/18890, ALFA)
A=0.07464 (1251/16760, 8.3KJPN)
A=0.1913 (1225/6404, 1000G_30x)
A=0.1877 (940/5008, 1000G)
A=0.2806 (1257/4480, Estonian)
A=0.3168 (1221/3854, ALSPAC)
A=0.3077 (1141/3708, TWINSUK)
A=0.1143 (335/2930, KOREAN)
A=0.1010 (185/1832, Korea1K)
A=0.304 (303/998, GoNL)
A=0.305 (183/600, NorthernSweden)
A=0.131 (70/536, SGDP_PRJ)
A=0.310 (67/216, Qatari)
A=0.150 (32/214, Vietnamese)
A=0.20 (9/44, Siberian)
A=0.42 (17/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LOC105372920 : 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=0.27401	G=0.72599
European	Sub	14286	A=0.30253	G=0.69747
African	Sub	2946	A=0.1687	G=0.8313
African Others	Sub	114	A=0.105	G=0.895
African American	Sub	2832	A=0.1713	G=0.8287
Asian	Sub	112	A=0.179	G=0.821
East Asian	Sub	86	A=0.16	G=0.84
Other Asian	Sub	26	A=0.23	G=0.77
Latin American 1	Sub	146	A=0.260	G=0.740
Latin American 2	Sub	610	A=0.167	G=0.833
South Asian	Sub	98	A=0.20	G=0.80
Other	Sub	692	A=0.256	G=0.744

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=0.243681	G=0.756319
gnomAD - Genomes	Global	Study-wide	139818	A=0.247143	G=0.752857
gnomAD - Genomes	European	Sub	75798	A=0.29898	G=0.70102
gnomAD - Genomes	African	Sub	41818	A=0.16660	G=0.83340
gnomAD - Genomes	American	Sub	13616	A=0.21365	G=0.78635
gnomAD - Genomes	Ashkenazi Jewish	Sub	3318	A=0.3162	G=0.6838
gnomAD - Genomes	East Asian	Sub	3118	A=0.1344	G=0.8656
gnomAD - Genomes	Other	Sub	2150	A=0.2553	G=0.7447
14KJPN	JAPANESE	Study-wide	28256	A=0.07574	G=0.92426
Allele Frequency Aggregator	Total	Global	18890	A=0.27401	G=0.72599
Allele Frequency Aggregator	European	Sub	14286	A=0.30253	G=0.69747
Allele Frequency Aggregator	African	Sub	2946	A=0.1687	G=0.8313
Allele Frequency Aggregator	Other	Sub	692	A=0.256	G=0.744
Allele Frequency Aggregator	Latin American 2	Sub	610	A=0.167	G=0.833
Allele Frequency Aggregator	Latin American 1	Sub	146	A=0.260	G=0.740
Allele Frequency Aggregator	Asian	Sub	112	A=0.179	G=0.821
Allele Frequency Aggregator	South Asian	Sub	98	A=0.20	G=0.80
8.3KJPN	JAPANESE	Study-wide	16760	A=0.07464	G=0.92536
1000Genomes_30x	Global	Study-wide	6404	A=0.1913	G=0.8087
1000Genomes_30x	African	Sub	1786	A=0.1517	G=0.8483
1000Genomes_30x	Europe	Sub	1266	A=0.2946	G=0.7054
1000Genomes_30x	South Asian	Sub	1202	A=0.1980	G=0.8020
1000Genomes_30x	East Asian	Sub	1170	A=0.1120	G=0.8880
1000Genomes_30x	American	Sub	980	A=0.216	G=0.784
1000Genomes	Global	Study-wide	5008	A=0.1877	G=0.8123
1000Genomes	African	Sub	1322	A=0.1490	G=0.8510
1000Genomes	East Asian	Sub	1008	A=0.1032	G=0.8968
1000Genomes	Europe	Sub	1006	A=0.2972	G=0.7028
1000Genomes	South Asian	Sub	978	A=0.190	G=0.810
1000Genomes	American	Sub	694	A=0.222	G=0.778
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.2806	G=0.7194
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.3168	G=0.6832
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.3077	G=0.6923
KOREAN population from KRGDB	KOREAN	Study-wide	2930	A=0.1143	G=0.8857
Korean Genome Project	KOREAN	Study-wide	1832	A=0.1010	G=0.8990
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.304	G=0.696
Northern Sweden	ACPOP	Study-wide	600	A=0.305	G=0.695
SGDP_PRJ	Global	Study-wide	536	A=0.131	G=0.869
Qatari	Global	Study-wide	216	A=0.310	G=0.690
A Vietnamese Genetic Variation Database	Global	Study-wide	214	A=0.150	G=0.850
Siberian	Global	Study-wide	44	A=0.20	G=0.80
The Danish reference pan genome	Danish	Study-wide	40	A=0.42	G=0.57

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 1	NC_000001.11:g.217188277A>G
GRCh37.p13 chr 1	NC_000001.10:g.217361619A>G

Gene: LOC105372920, uncharacterized LOC105372920 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105372920 transcript	XR_922600.2: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	A=	G
GRCh38.p14 chr 1	NC_000001.11:g.217188277=	NC_000001.11:g.217188277A>G
GRCh37.p13 chr 1	NC_000001.10:g.217361619=	NC_000001.10:g.217361619A>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#.

75 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	BCM_SSAHASNP	ss9838534	Jul 11, 2003 (116)
2	SC_JCM	ss11200285	Jul 11, 2003 (116)
3	WI_SSAHASNP	ss11369433	Jul 11, 2003 (116)
4	CSHL-HAPMAP	ss16384109	Feb 27, 2004 (120)
5	SSAHASNP	ss20429342	Apr 05, 2004 (121)
6	ABI	ss41289169	Mar 15, 2006 (126)
7	HGSV	ss80194858	Dec 14, 2007 (130)
8	HGSV	ss83453895	Dec 14, 2007 (130)
9	BCMHGSC_JDW	ss87971094	Mar 23, 2008 (129)
10	HUMANGENOME_JCVI	ss98004305	Feb 04, 2009 (130)
11	BGI	ss106632483	Feb 04, 2009 (130)
12	1000GENOMES	ss108948084	Jan 23, 2009 (130)
13	ILLUMINA-UK	ss119208544	Dec 01, 2009 (131)
14	ENSEMBL	ss138154549	Dec 01, 2009 (131)
15	ENSEMBL	ss139068181	Dec 01, 2009 (131)
16	GMI	ss156287466	Dec 01, 2009 (131)
17	COMPLETE_GENOMICS	ss165160066	Jul 04, 2010 (132)
18	BUSHMAN	ss199613069	Jul 04, 2010 (132)
19	BCM-HGSC-SUB	ss205470729	Jul 04, 2010 (132)
20	1000GENOMES	ss210740507	Jul 14, 2010 (132)
21	1000GENOMES	ss218883615	Jul 14, 2010 (132)
22	1000GENOMES	ss230903143	Jul 14, 2010 (132)
23	1000GENOMES	ss238515214	Jul 15, 2010 (132)
24	GMI	ss276217767	May 04, 2012 (137)
25	GMI	ss284229044	Apr 25, 2013 (138)
26	PJP	ss290734449	May 09, 2011 (134)
27	TISHKOFF	ss555140926	Apr 25, 2013 (138)
28	SSMP	ss648702690	Apr 25, 2013 (138)
29	EVA-GONL	ss976147190	Aug 21, 2014 (142)
30	JMKIDD_LAB	ss1068603512	Aug 21, 2014 (142)
31	1000GENOMES	ss1294661384	Aug 21, 2014 (142)
32	DDI	ss1426112121	Apr 01, 2015 (144)
33	EVA_GENOME_DK	ss1574681238	Apr 01, 2015 (144)
34	EVA_UK10K_ALSPAC	ss1602146553	Apr 01, 2015 (144)
35	EVA_UK10K_TWINSUK	ss1645140586	Apr 01, 2015 (144)
36	HAMMER_LAB	ss1795732172	Sep 08, 2015 (146)
37	WEILL_CORNELL_DGM	ss1919371172	Feb 12, 2016 (147)
38	JJLAB	ss2020208276	Sep 14, 2016 (149)
39	USC_VALOUEV	ss2148239182	Dec 20, 2016 (150)
40	HUMAN_LONGEVITY	ss2170111294	Dec 20, 2016 (150)
41	SYSTEMSBIOZJU	ss2624613221	Nov 08, 2017 (151)
42	GRF	ss2698233140	Nov 08, 2017 (151)
43	GNOMAD	ss2766242408	Nov 08, 2017 (151)
44	SWEGEN	ss2988454658	Nov 08, 2017 (151)
45	BIOINF_KMB_FNS_UNIBA	ss3023863934	Nov 08, 2017 (151)
46	CSHL	ss3343912721	Nov 08, 2017 (151)
47	URBANLAB	ss3646887757	Oct 11, 2018 (152)
48	EGCUT_WGS	ss3656415293	Jul 12, 2019 (153)
49	EVA_DECODE	ss3688635163	Jul 12, 2019 (153)
50	ACPOP	ss3727865025	Jul 12, 2019 (153)
51	EVA	ss3747338441	Jul 12, 2019 (153)
52	PACBIO	ss3783687167	Jul 12, 2019 (153)
53	PACBIO	ss3789299178	Jul 12, 2019 (153)
54	PACBIO	ss3794171472	Jul 12, 2019 (153)
55	KHV_HUMAN_GENOMES	ss3800342833	Jul 12, 2019 (153)
56	EVA	ss3826644626	Apr 25, 2020 (154)
57	EVA	ss3836722773	Apr 25, 2020 (154)
58	EVA	ss3842134604	Apr 25, 2020 (154)
59	SGDP_PRJ	ss3850902827	Apr 25, 2020 (154)
60	KRGDB	ss3896218108	Apr 25, 2020 (154)
61	KOGIC	ss3946497057	Apr 25, 2020 (154)
62	TOPMED	ss4483664424	Apr 27, 2021 (155)
63	TOMMO_GENOMICS	ss5148442510	Apr 27, 2021 (155)
64	1000G_HIGH_COVERAGE	ss5245805838	Oct 12, 2022 (156)
65	EVA	ss5324809911	Oct 12, 2022 (156)
66	EVA	ss5506186581	Oct 12, 2022 (156)
67	1000G_HIGH_COVERAGE	ss5519908948	Oct 12, 2022 (156)
68	SANFORD_IMAGENETICS	ss5627453964	Oct 12, 2022 (156)
69	TOMMO_GENOMICS	ss5676206809	Oct 12, 2022 (156)
70	YY_MCH	ss5801639566	Oct 12, 2022 (156)
71	EVA	ss5833264835	Oct 12, 2022 (156)
72	EVA	ss5849285341	Oct 12, 2022 (156)
73	EVA	ss5911987098	Oct 12, 2022 (156)
74	EVA	ss5939291942	Oct 12, 2022 (156)
75	EVA	ss5980015026	Oct 12, 2022 (156)
76	1000Genomes	NC_000001.10 - 217361619	Oct 11, 2018 (152)
77	1000Genomes_30x	NC_000001.11 - 217188277	Oct 12, 2022 (156)
78	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 217361619	Oct 11, 2018 (152)
79	Genetic variation in the Estonian population	NC_000001.10 - 217361619	Oct 11, 2018 (152)
80	The Danish reference pan genome	NC_000001.10 - 217361619	Apr 25, 2020 (154)
81	gnomAD - Genomes	NC_000001.11 - 217188277	Apr 27, 2021 (155)
82	Genome of the Netherlands Release 5	NC_000001.10 - 217361619	Apr 25, 2020 (154)
83	KOREAN population from KRGDB	NC_000001.10 - 217361619	Apr 25, 2020 (154)
84	Korean Genome Project	NC_000001.11 - 217188277	Apr 25, 2020 (154)
85	Northern Sweden	NC_000001.10 - 217361619	Jul 12, 2019 (153)
86	Qatari	NC_000001.10 - 217361619	Apr 25, 2020 (154)
87	SGDP_PRJ	NC_000001.10 - 217361619	Apr 25, 2020 (154)
88	Siberian	NC_000001.10 - 217361619	Apr 25, 2020 (154)
89	8.3KJPN	NC_000001.10 - 217361619	Apr 27, 2021 (155)
90	14KJPN	NC_000001.11 - 217188277	Oct 12, 2022 (156)
91	TopMed	NC_000001.11 - 217188277	Apr 27, 2021 (155)
92	UK 10K study - Twins	NC_000001.10 - 217361619	Oct 11, 2018 (152)
93	A Vietnamese Genetic Variation Database	NC_000001.10 - 217361619	Jul 12, 2019 (153)
94	ALFA	NC_000001.11 - 217188277	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)
rs57348485	May 23, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss80194858, ss83453895	NC_000001.8:213750013:A:G	NC_000001.11:217188276:A:G	(self)
ss87971094, ss108948084, ss119208544, ss165160066, ss199613069, ss205470729, ss210740507, ss276217767, ss284229044, ss290734449	NC_000001.9:215428241:A:G	NC_000001.11:217188276:A:G	(self)
5516313, 3046295, 2153541, 1885525, 1330392, 3395502, 1149890, 1413102, 2919807, 755536, 6411817, 3046295, 659028, ss218883615, ss230903143, ss238515214, ss555140926, ss648702690, ss976147190, ss1068603512, ss1294661384, ss1426112121, ss1574681238, ss1602146553, ss1645140586, ss1795732172, ss1919371172, ss2020208276, ss2148239182, ss2624613221, ss2698233140, ss2766242408, ss2988454658, ss3343912721, ss3656415293, ss3727865025, ss3747338441, ss3783687167, ss3789299178, ss3794171472, ss3826644626, ss3836722773, ss3850902827, ss3896218108, ss5148442510, ss5324809911, ss5506186581, ss5627453964, ss5833264835, ss5939291942, ss5980015026	NC_000001.10:217361618:A:G	NC_000001.11:217188276:A:G	(self)
7434883, 39652567, 2875058, 10043913, 47270759, 12570014369, ss2170111294, ss3023863934, ss3646887757, ss3688635163, ss3800342833, ss3842134604, ss3946497057, ss4483664424, ss5245805838, ss5519908948, ss5676206809, ss5801639566, ss5849285341, ss5911987098	NC_000001.11:217188276:A:G	NC_000001.11:217188276:A:G	(self)
ss16384109, ss20429342	NT_021877.16:10797524:A:G	NC_000001.11:217188276:A:G	(self)
ss9838534, ss11200285, ss11369433	NT_077937.1:919739:A:G	NC_000001.11:217188276:A:G	(self)
ss41289169, ss98004305, ss106632483, ss138154549, ss139068181, ss156287466	NT_167186.1:10879397:A:G	NC_000001.11:217188276: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 rs6422639

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

rs6422639