Name: rs2613508
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.

rs2613508

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:72367899 (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>G / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.146046 (38657/264690, TOPMED)
C=0.153624 (21508/140004, GnomAD)
C=0.02593 (732/28232, 14KJPN) (+ 16 more)
C=0.16223 (2878/17740, ALFA)
C=0.02768 (464/16760, 8.3KJPN)
C=0.1017 (651/6404, 1000G_30x)
C=0.1022 (512/5008, 1000G)
C=0.1540 (690/4480, Estonian)
C=0.1959 (755/3854, ALSPAC)
C=0.2157 (800/3708, TWINSUK)
C=0.0130 (38/2930, KOREAN)
C=0.0186 (34/1832, Korea1K)
C=0.195 (195/998, GoNL)
C=0.218 (131/600, NorthernSweden)
C=0.058 (32/556, SGDP_PRJ)
C=0.088 (19/216, Qatari)
C=0.033 (7/214, Vietnamese)
C=0.15 (8/54, Siberian)
C=0.23 (9/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LOC105378797 : 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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	Alt HMOZ	HTRZ	HWEP
Total	Global	17740	C=0.16223	G=0.00000, T=0.83777	0.028298	0.703833	0.267869	1
European	Sub	13642	C=0.16962	G=0.00000, T=0.83038	0.029028	0.689782	0.28119	0
African	Sub	2444	C=0.1530	G=0.0000, T=0.8470	0.030278	0.724223	0.245499	2
African Others	Sub	90	C=0.14	G=0.00, T=0.86	0.022222	0.733333	0.244444	0
African American	Sub	2354	C=0.1534	G=0.0000, T=0.8466	0.030586	0.723874	0.24554	2
Asian	Sub	112	C=0.018	G=0.000, T=0.982	0.0	0.964286	0.035714	0
East Asian	Sub	86	C=0.02	G=0.00, T=0.98	0.0	0.953488	0.046512	0
Other Asian	Sub	26	C=0.00	G=0.00, T=1.00	0.0	1.0	0.0	N/A
Latin American 1	Sub	146	C=0.130	G=0.000, T=0.870	0.027397	0.767123	0.205479	0
Latin American 2	Sub	610	C=0.092	G=0.000, T=0.908	0.013115	0.829508	0.157377	1
South Asian	Sub	98	C=0.11	G=0.00, T=0.89	0.020408	0.795918	0.183673	0
Other	Sub	688	C=0.148	G=0.000, T=0.852	0.026163	0.729651	0.244186	0

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=0.146046	T=0.853954
gnomAD - Genomes	Global	Study-wide	140004	C=0.153624	T=0.846376
gnomAD - Genomes	European	Sub	75834	C=0.17437	T=0.82563
gnomAD - Genomes	African	Sub	41974	C=0.14385	T=0.85615
gnomAD - Genomes	American	Sub	13600	C=0.11382	T=0.88618
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	C=0.1080	T=0.8920
gnomAD - Genomes	East Asian	Sub	3126	C=0.0150	T=0.9850
gnomAD - Genomes	Other	Sub	2146	C=0.1365	T=0.8635
14KJPN	JAPANESE	Study-wide	28232	C=0.02593	T=0.97407
Allele Frequency Aggregator	Total	Global	17740	C=0.16223	G=0.00000, T=0.83777
Allele Frequency Aggregator	European	Sub	13642	C=0.16962	G=0.00000, T=0.83038
Allele Frequency Aggregator	African	Sub	2444	C=0.1530	G=0.0000, T=0.8470
Allele Frequency Aggregator	Other	Sub	688	C=0.148	G=0.000, T=0.852
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.092	G=0.000, T=0.908
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.130	G=0.000, T=0.870
Allele Frequency Aggregator	Asian	Sub	112	C=0.018	G=0.000, T=0.982
Allele Frequency Aggregator	South Asian	Sub	98	C=0.11	G=0.00, T=0.89
8.3KJPN	JAPANESE	Study-wide	16760	C=0.02768	T=0.97232
1000Genomes_30x	Global	Study-wide	6404	C=0.1017	T=0.8983
1000Genomes_30x	African	Sub	1786	C=0.1501	T=0.8499
1000Genomes_30x	Europe	Sub	1266	C=0.1722	T=0.8278
1000Genomes_30x	South Asian	Sub	1202	C=0.0499	T=0.9501
1000Genomes_30x	East Asian	Sub	1170	C=0.0162	T=0.9838
1000Genomes_30x	American	Sub	980	C=0.088	T=0.912
1000Genomes	Global	Study-wide	5008	C=0.1022	T=0.8978
1000Genomes	African	Sub	1322	C=0.1543	T=0.8457
1000Genomes	East Asian	Sub	1008	C=0.0159	T=0.9841
1000Genomes	Europe	Sub	1006	C=0.1789	T=0.8211
1000Genomes	South Asian	Sub	978	C=0.055	T=0.945
1000Genomes	American	Sub	694	C=0.084	T=0.916
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.1540	T=0.8460
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.1959	T=0.8041
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.2157	T=0.7843
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.0130	G=0.0000, T=0.9870
Korean Genome Project	KOREAN	Study-wide	1832	C=0.0186	T=0.9814
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.195	T=0.805
Northern Sweden	ACPOP	Study-wide	600	C=0.218	T=0.782
SGDP_PRJ	Global	Study-wide	556	C=0.058	T=0.942
Qatari	Global	Study-wide	216	C=0.088	T=0.912
A Vietnamese Genetic Variation Database	Global	Study-wide	214	C=0.033	T=0.967
Siberian	Global	Study-wide	54	C=0.15	T=0.85
The Danish reference pan genome	Danish	Study-wide	40	C=0.23	T=0.78

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.72367899C>G
GRCh38.p14 chr 1	NC_000001.11:g.72367899C>T
GRCh37.p13 chr 1	NC_000001.10:g.72833582C>G
GRCh37.p13 chr 1	NC_000001.10:g.72833582C>T
GRCh38.p14 chr 1 novel patch HSCHR1_9_CTG3	NW_018654707.1:g.89124C>G
GRCh38.p14 chr 1 novel patch HSCHR1_9_CTG3	NW_018654707.1:g.89124C>T

Gene: LOC105378797, uncharacterized LOC105378797 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105378797 transcript variant X2	XR_001737670.2:n.	N/A	Intron Variant
LOC105378797 transcript variant X4	XR_001737671.3:n.	N/A	Intron Variant
LOC105378797 transcript variant X1	XR_947505.3:n.	N/A	Intron Variant
LOC105378797 transcript variant X3	XR_947506.3: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=	G	T
GRCh38.p14 chr 1	NC_000001.11:g.72367899=	NC_000001.11:g.72367899C>G	NC_000001.11:g.72367899C>T
GRCh37.p13 chr 1	NC_000001.10:g.72833582=	NC_000001.10:g.72833582C>G	NC_000001.10:g.72833582C>T
GRCh38.p14 chr 1 novel patch HSCHR1_9_CTG3	NW_018654707.1:g.89124=	NW_018654707.1:g.89124C>G	NW_018654707.1:g.89124C>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#.

75 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss3678416	Sep 28, 2001 (100)
2	SC_JCM	ss5859155	Feb 20, 2003 (126)
3	CSHL-HAPMAP	ss17350657	Feb 27, 2004 (126)
4	ABI	ss41261422	Mar 11, 2006 (126)
5	HGSV	ss78265086	Dec 06, 2007 (129)
6	HUMANGENOME_JCVI	ss99217228	Feb 06, 2009 (130)
7	BGI	ss106575561	Feb 06, 2009 (130)
8	1000GENOMES	ss108302775	Jan 23, 2009 (130)
9	1000GENOMES	ss110627824	Jan 25, 2009 (130)
10	ILLUMINA-UK	ss118796150	Dec 01, 2009 (131)
11	ENSEMBL	ss143853802	Dec 01, 2009 (131)
12	GMI	ss155164229	Dec 01, 2009 (131)
13	COMPLETE_GENOMICS	ss163505637	Jul 04, 2010 (132)
14	COMPLETE_GENOMICS	ss164532621	Jul 04, 2010 (132)
15	COMPLETE_GENOMICS	ss166683926	Jul 04, 2010 (132)
16	BUSHMAN	ss198609226	Jul 04, 2010 (132)
17	BCM-HGSC-SUB	ss205178665	Jul 04, 2010 (132)
18	1000GENOMES	ss218450547	Jul 14, 2010 (132)
19	1000GENOMES	ss230582263	Jul 14, 2010 (132)
20	1000GENOMES	ss238267098	Jul 15, 2010 (132)
21	BL	ss253178241	May 09, 2011 (134)
22	GMI	ss275873040	May 04, 2012 (137)
23	GMI	ss284071432	Apr 25, 2013 (138)
24	PJP	ss290535396	May 09, 2011 (134)
25	TISHKOFF	ss554240973	Apr 25, 2013 (138)
26	SSMP	ss648123211	Apr 25, 2013 (138)
27	EVA-GONL	ss975284108	Aug 21, 2014 (142)
28	JMKIDD_LAB	ss1067982318	Aug 21, 2014 (142)
29	1000GENOMES	ss1291368282	Aug 21, 2014 (142)
30	DDI	ss1425849422	Apr 01, 2015 (144)
31	EVA_GENOME_DK	ss1574142099	Apr 01, 2015 (144)
32	EVA_DECODE	ss1584655763	Apr 01, 2015 (144)
33	EVA_UK10K_ALSPAC	ss1600426499	Apr 01, 2015 (144)
34	EVA_UK10K_TWINSUK	ss1643420532	Apr 01, 2015 (144)
35	HAMMER_LAB	ss1794544168	Sep 08, 2015 (146)
36	WEILL_CORNELL_DGM	ss1918490757	Feb 12, 2016 (147)
37	GENOMED	ss1966775258	Jul 19, 2016 (147)
38	JJLAB	ss2019763272	Sep 14, 2016 (149)
39	USC_VALOUEV	ss2147779655	Dec 20, 2016 (150)
40	HUMAN_LONGEVITY	ss2163502302	Dec 20, 2016 (150)
41	SYSTEMSBIOZJU	ss2624394663	Nov 08, 2017 (151)
42	GRF	ss2697699276	Nov 08, 2017 (151)
43	GNOMAD	ss2756504521	Nov 08, 2017 (151)
44	SWEGEN	ss2987005748	Nov 08, 2017 (151)
45	BIOINF_KMB_FNS_UNIBA	ss3023643599	Nov 08, 2017 (151)
46	CSHL	ss3343508771	Nov 08, 2017 (151)
47	URBANLAB	ss3646688544	Oct 11, 2018 (152)
48	EGCUT_WGS	ss3655079315	Jul 12, 2019 (153)
49	EVA_DECODE	ss3687004912	Jul 12, 2019 (153)
50	ACPOP	ss3727150466	Jul 12, 2019 (153)
51	EVA	ss3746349795	Jul 12, 2019 (153)
52	PACBIO	ss3783442946	Jul 12, 2019 (153)
53	PACBIO	ss3789096062	Jul 12, 2019 (153)
54	PACBIO	ss3793968814	Jul 12, 2019 (153)
55	KHV_HUMAN_GENOMES	ss3799355927	Jul 12, 2019 (153)
56	EVA	ss3826232512	Apr 25, 2020 (154)
57	EVA	ss3836504062	Apr 25, 2020 (154)
58	EVA	ss3841910795	Apr 25, 2020 (154)
59	SGDP_PRJ	ss3849094325	Apr 25, 2020 (154)
60	KRGDB	ss3894130871	Apr 25, 2020 (154)
61	KOGIC	ss3944742542	Apr 25, 2020 (154)
62	TOPMED	ss4453994527	Apr 25, 2021 (155)
63	TOMMO_GENOMICS	ss5144482583	Apr 25, 2021 (155)
64	1000G_HIGH_COVERAGE	ss5242680956	Oct 12, 2022 (156)
65	EVA	ss5319491786	Oct 12, 2022 (156)
66	HUGCELL_USP	ss5443704413	Oct 12, 2022 (156)
67	EVA	ss5505892799	Oct 12, 2022 (156)
68	1000G_HIGH_COVERAGE	ss5515173439	Oct 12, 2022 (156)
69	SANFORD_IMAGENETICS	ss5625765262	Oct 12, 2022 (156)
70	TOMMO_GENOMICS	ss5669406514	Oct 12, 2022 (156)
71	YY_MCH	ss5800698951	Oct 12, 2022 (156)
72	EVA	ss5832118487	Oct 12, 2022 (156)
73	EVA	ss5848956259	Oct 12, 2022 (156)
74	EVA	ss5908737354	Oct 12, 2022 (156)
75	EVA	ss5937607334	Oct 12, 2022 (156)
76	1000Genomes	NC_000001.10 - 72833582	Oct 11, 2018 (152)
77	1000Genomes_30x	NC_000001.11 - 72367899	Oct 12, 2022 (156)
78	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 72833582	Oct 11, 2018 (152)
79	Genetic variation in the Estonian population	NC_000001.10 - 72833582	Oct 11, 2018 (152)
80	The Danish reference pan genome	NC_000001.10 - 72833582	Apr 25, 2020 (154)
81	gnomAD - Genomes	NC_000001.11 - 72367899	Apr 25, 2021 (155)
82	Genome of the Netherlands Release 5	NC_000001.10 - 72833582	Apr 25, 2020 (154)
83	KOREAN population from KRGDB	NC_000001.10 - 72833582	Apr 25, 2020 (154)
84	Korean Genome Project	NC_000001.11 - 72367899	Apr 25, 2020 (154)
85	Northern Sweden	NC_000001.10 - 72833582	Jul 12, 2019 (153)
86	Qatari	NC_000001.10 - 72833582	Apr 25, 2020 (154)
87	SGDP_PRJ	NC_000001.10 - 72833582	Apr 25, 2020 (154)
88	Siberian	NC_000001.10 - 72833582	Apr 25, 2020 (154)
89	8.3KJPN	NC_000001.10 - 72833582	Apr 25, 2021 (155)
90	14KJPN	NC_000001.11 - 72367899	Oct 12, 2022 (156)
91	TopMed	NC_000001.11 - 72367899	Apr 25, 2021 (155)
92	UK 10K study - Twins	NC_000001.10 - 72833582	Oct 11, 2018 (152)
93	A Vietnamese Genetic Variation Database	NC_000001.10 - 72833582	Jul 12, 2019 (153)
94	ALFA	NC_000001.11 - 72367899	Apr 25, 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)
rs4388646	Mar 11, 2006 (126)
rs5013846	Mar 11, 2006 (126)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
1308265, ss3894130871	NC_000001.10:72833581:C:G	NC_000001.11:72367898:C:G	(self)
11166887746	NC_000001.11:72367898:C:G	NC_000001.11:72367898:C:G	(self)
ss78265086	NC_000001.8:72545602:C:T	NC_000001.11:72367898:C:T	(self)
ss108302775, ss110627824, ss118796150, ss163505637, ss164532621, ss166683926, ss198609226, ss205178665, ss253178241, ss275873040, ss284071432, ss290535396, ss1584655763	NC_000001.9:72606169:C:T	NC_000001.11:72367898:C:T	(self)
2103995, 1154058, 817563, 1550572, 492674, 1308265, 435331, 532687, 1111305, 296009, 2451890, 1154058, 242422, ss218450547, ss230582263, ss238267098, ss554240973, ss648123211, ss975284108, ss1067982318, ss1291368282, ss1425849422, ss1574142099, ss1600426499, ss1643420532, ss1794544168, ss1918490757, ss1966775258, ss2019763272, ss2147779655, ss2624394663, ss2697699276, ss2756504521, ss2987005748, ss3343508771, ss3655079315, ss3727150466, ss3746349795, ss3783442946, ss3789096062, ss3793968814, ss3826232512, ss3836504062, ss3849094325, ss3894130871, ss5144482583, ss5319491786, ss5505892799, ss5625765262, ss5832118487, ss5937607334	NC_000001.10:72833581:C:T	NC_000001.11:72367898:C:T	(self)
2699374, 14866045, 1120543, 3243618, 17600862, 11166887746, ss2163502302, ss3023643599, ss3646688544, ss3687004912, ss3799355927, ss3841910795, ss3944742542, ss4453994527, ss5242680956, ss5443704413, ss5515173439, ss5669406514, ss5800698951, ss5848956259, ss5908737354	NC_000001.11:72367898:C:T	NC_000001.11:72367898:C:T	(self)
ss17350657	NT_032977.6:34396650:C:T	NC_000001.11:72367898:C:T	(self)
ss3678416, ss5859155, ss41261422, ss99217228, ss106575561, ss143853802, ss155164229	NT_032977.9:42805499:C:T	NC_000001.11:72367898: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 rs2613508

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

rs2613508