Name: rs3861552
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.

rs3861552

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr19:254899 (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=0.349409 (92485/264690, TOPMED)
A=0.335460 (47006/140124, GnomAD)
G=0.17719 (5007/28258, 14KJPN) (+ 15 more)
A=0.35093 (6629/18890, ALFA)
G=0.17906 (3001/16760, 8.3KJPN)
A=0.4422 (2832/6404, 1000G_30x)
A=0.4543 (2275/5008, 1000G)
A=0.4172 (1608/3854, ALSPAC)
A=0.4075 (1511/3708, TWINSUK)
G=0.1701 (497/2922, KOREAN)
G=0.1758 (322/1832, Korea1K)
A=0.418 (417/998, GoNL)
A=0.420 (252/600, NorthernSweden)
G=0.416 (222/534, MGP)
A=0.254 (95/374, SGDP_PRJ)
A=0.370 (80/216, Qatari)
G=0.120 (26/216, Vietnamese)
A=0.33 (14/42, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: None
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=0.35093	G=0.64907
European	Sub	14286	A=0.38310	G=0.61690
African	Sub	2946	A=0.1432	G=0.8568
African Others	Sub	114	A=0.079	G=0.921
African American	Sub	2832	A=0.1458	G=0.8542
Asian	Sub	112	A=0.848	G=0.152
East Asian	Sub	86	A=0.90	G=0.10
Other Asian	Sub	26	A=0.69	G=0.31
Latin American 1	Sub	146	A=0.322	G=0.678
Latin American 2	Sub	610	A=0.489	G=0.511
South Asian	Sub	98	A=0.55	G=0.45
Other	Sub	692	A=0.347	G=0.653

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=0.349409	G=0.650591
gnomAD - Genomes	Global	Study-wide	140124	A=0.335460	G=0.664540
gnomAD - Genomes	European	Sub	75880	A=0.39432	G=0.60568
gnomAD - Genomes	African	Sub	42014	A=0.14955	G=0.85045
gnomAD - Genomes	American	Sub	13628	A=0.46030	G=0.53970
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	A=0.3087	G=0.6913
gnomAD - Genomes	East Asian	Sub	3126	A=0.8704	G=0.1296
gnomAD - Genomes	Other	Sub	2152	A=0.3634	G=0.6366
14KJPN	JAPANESE	Study-wide	28258	A=0.82281	G=0.17719
Allele Frequency Aggregator	Total	Global	18890	A=0.35093	G=0.64907
Allele Frequency Aggregator	European	Sub	14286	A=0.38310	G=0.61690
Allele Frequency Aggregator	African	Sub	2946	A=0.1432	G=0.8568
Allele Frequency Aggregator	Other	Sub	692	A=0.347	G=0.653
Allele Frequency Aggregator	Latin American 2	Sub	610	A=0.489	G=0.511
Allele Frequency Aggregator	Latin American 1	Sub	146	A=0.322	G=0.678
Allele Frequency Aggregator	Asian	Sub	112	A=0.848	G=0.152
Allele Frequency Aggregator	South Asian	Sub	98	A=0.55	G=0.45
8.3KJPN	JAPANESE	Study-wide	16760	A=0.82094	G=0.17906
1000Genomes_30x	Global	Study-wide	6404	A=0.4422	G=0.5578
1000Genomes_30x	African	Sub	1786	A=0.1120	G=0.8880
1000Genomes_30x	Europe	Sub	1266	A=0.3768	G=0.6232
1000Genomes_30x	South Asian	Sub	1202	A=0.5416	G=0.4584
1000Genomes_30x	East Asian	Sub	1170	A=0.8718	G=0.1282
1000Genomes_30x	American	Sub	980	A=0.494	G=0.506
1000Genomes	Global	Study-wide	5008	A=0.4543	G=0.5457
1000Genomes	African	Sub	1322	A=0.1165	G=0.8835
1000Genomes	East Asian	Sub	1008	A=0.8760	G=0.1240
1000Genomes	Europe	Sub	1006	A=0.3738	G=0.6262
1000Genomes	South Asian	Sub	978	A=0.532	G=0.468
1000Genomes	American	Sub	694	A=0.493	G=0.507
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.4172	G=0.5828
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.4075	G=0.5925
KOREAN population from KRGDB	KOREAN	Study-wide	2922	A=0.8299	G=0.1701
Korean Genome Project	KOREAN	Study-wide	1832	A=0.8242	G=0.1758
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.418	G=0.582
Northern Sweden	ACPOP	Study-wide	600	A=0.420	G=0.580
Medical Genome Project healthy controls from Spanish population	Spanish controls	Study-wide	534	A=0.584	G=0.416
SGDP_PRJ	Global	Study-wide	374	A=0.254	G=0.746
Qatari	Global	Study-wide	216	A=0.370	G=0.630
A Vietnamese Genetic Variation Database	Global	Study-wide	216	A=0.880	G=0.120
Siberian	Global	Study-wide	42	A=0.33	G=0.67

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 19	NC_000019.10:g.254899A>G
GRCh37.p13 chr 19	NC_000019.9:g.254899A>G

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 19	NC_000019.10:g.254899=	NC_000019.10:g.254899A>G
GRCh37.p13 chr 19	NC_000019.9:g.254899=	NC_000019.9:g.254899A>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#.

61 SubSNP, 18 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss5269992	Oct 08, 2002 (108)
2	TSC-CSHL	ss5520287	Oct 08, 2002 (108)
3	SC_JCM	ss5819563	Feb 20, 2003 (111)
4	WI_SSAHASNP	ss6768373	Feb 20, 2003 (111)
5	BCM_SSAHASNP	ss14705871	Dec 05, 2003 (119)
6	ABI	ss40995080	Mar 14, 2006 (126)
7	HGSV	ss77262142	Dec 07, 2007 (129)
8	HGSV	ss81940711	Dec 16, 2007 (130)
9	HGSV	ss84669225	Dec 16, 2007 (130)
10	HUMANGENOME_JCVI	ss96284283	Feb 06, 2009 (130)
11	ILLUMINA-UK	ss117613082	Feb 14, 2009 (130)
12	ENSEMBL	ss132738411	Dec 01, 2009 (131)
13	BUSHMAN	ss203566700	Jul 04, 2010 (132)
14	1000GENOMES	ss243800870	Jul 15, 2010 (132)
15	BL	ss255419699	May 09, 2011 (134)
16	GMI	ss283092183	May 04, 2012 (137)
17	PJP	ss292171233	May 09, 2011 (134)
18	SSMP	ss661648822	Apr 25, 2013 (138)
19	EVA-GONL	ss993995675	Aug 21, 2014 (142)
20	JMKIDD_LAB	ss1081702578	Aug 21, 2014 (142)
21	1000GENOMES	ss1362000491	Aug 21, 2014 (142)
22	DDI	ss1428306255	Apr 01, 2015 (144)
23	EVA_UK10K_ALSPAC	ss1637405221	Apr 01, 2015 (144)
24	EVA_UK10K_TWINSUK	ss1680399254	Apr 01, 2015 (144)
25	EVA_DECODE	ss1698059255	Apr 01, 2015 (144)
26	EVA_MGP	ss1711490237	Apr 01, 2015 (144)
27	HAMMER_LAB	ss1809165862	Sep 08, 2015 (146)
28	WEILL_CORNELL_DGM	ss1937469562	Feb 12, 2016 (147)
29	GENOMED	ss1968590693	Jul 19, 2016 (147)
30	JJLAB	ss2029511266	Sep 14, 2016 (149)
31	USC_VALOUEV	ss2158020202	Dec 20, 2016 (150)
32	GRF	ss2702623896	Nov 08, 2017 (151)
33	GNOMAD	ss2959412280	Nov 08, 2017 (151)
34	SWEGEN	ss3016931904	Nov 08, 2017 (151)
35	CSHL	ss3352151277	Nov 08, 2017 (151)
36	URBANLAB	ss3650849044	Oct 12, 2018 (152)
37	EVA_DECODE	ss3702151191	Jul 13, 2019 (153)
38	ACPOP	ss3742772465	Jul 13, 2019 (153)
39	EVA	ss3755703541	Jul 13, 2019 (153)
40	PACBIO	ss3788442848	Jul 13, 2019 (153)
41	PACBIO	ss3793366381	Jul 13, 2019 (153)
42	PACBIO	ss3798252960	Jul 13, 2019 (153)
43	KHV_HUMAN_GENOMES	ss3820957698	Jul 13, 2019 (153)
44	EVA	ss3835302393	Apr 27, 2020 (154)
45	EVA	ss3841274036	Apr 27, 2020 (154)
46	EVA	ss3846777696	Apr 27, 2020 (154)
47	SGDP_PRJ	ss3887550946	Apr 27, 2020 (154)
48	KRGDB	ss3937466260	Apr 27, 2020 (154)
49	KOGIC	ss3980611356	Apr 27, 2020 (154)
50	TOPMED	ss5065094061	Apr 26, 2021 (155)
51	TOMMO_GENOMICS	ss5226273542	Apr 26, 2021 (155)
52	1000G_HIGH_COVERAGE	ss5306152318	Oct 16, 2022 (156)
53	EVA	ss5512026741	Oct 16, 2022 (156)
54	1000G_HIGH_COVERAGE	ss5611422616	Oct 16, 2022 (156)
55	SANFORD_IMAGENETICS	ss5661794032	Oct 16, 2022 (156)
56	TOMMO_GENOMICS	ss5784383281	Oct 16, 2022 (156)
57	YY_MCH	ss5817322606	Oct 16, 2022 (156)
58	EVA	ss5840122552	Oct 16, 2022 (156)
59	EVA	ss5852168448	Oct 16, 2022 (156)
60	EVA	ss5926949359	Oct 16, 2022 (156)
61	EVA	ss5953228510	Oct 16, 2022 (156)
62	1000Genomes	NC_000019.9 - 254899	Oct 12, 2018 (152)
63	1000Genomes_30x	NC_000019.10 - 254899	Oct 16, 2022 (156)
64	The Avon Longitudinal Study of Parents and Children	NC_000019.9 - 254899	Oct 12, 2018 (152)
65	gnomAD - Genomes	NC_000019.10 - 254899	Apr 26, 2021 (155)
66	Genome of the Netherlands Release 5	NC_000019.9 - 254899	Apr 27, 2020 (154)
67	KOREAN population from KRGDB	NC_000019.9 - 254899	Apr 27, 2020 (154)
68	Korean Genome Project	NC_000019.10 - 254899	Apr 27, 2020 (154)
69	Medical Genome Project healthy controls from Spanish population	NC_000019.9 - 254899	Apr 27, 2020 (154)
70	Northern Sweden	NC_000019.9 - 254899	Jul 13, 2019 (153)
71	Qatari	NC_000019.9 - 254899	Apr 27, 2020 (154)
72	SGDP_PRJ	NC_000019.9 - 254899	Apr 27, 2020 (154)
73	Siberian	NC_000019.9 - 254899	Apr 27, 2020 (154)
74	8.3KJPN	NC_000019.9 - 254899	Apr 26, 2021 (155)
75	14KJPN	NC_000019.10 - 254899	Oct 16, 2022 (156)
76	TopMed	NC_000019.10 - 254899	Apr 26, 2021 (155)
77	UK 10K study - Twins	NC_000019.9 - 254899	Oct 12, 2018 (152)
78	A Vietnamese Genetic Variation Database	NC_000019.9 - 254899	Jul 13, 2019 (153)
79	ALFA	NC_000019.10 - 254899	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)
rs61388906	May 26, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss77262142, ss81940711, ss84669225, ss117613082, ss203566700, ss255419699, ss283092183, ss292171233, ss1698059255	NC_000019.8:205898:A:G	NC_000019.10:254898:A:G	(self)
75364712, 41781267, 18616193, 44643654, 605997, 16057330, 19511484, 39567926, 10536556, 84242849, 41781267, 9240208, ss243800870, ss661648822, ss993995675, ss1081702578, ss1362000491, ss1428306255, ss1637405221, ss1680399254, ss1711490237, ss1809165862, ss1937469562, ss1968590693, ss2029511266, ss2158020202, ss2702623896, ss2959412280, ss3016931904, ss3352151277, ss3742772465, ss3755703541, ss3788442848, ss3793366381, ss3798252960, ss3835302393, ss3841274036, ss3887550946, ss3937466260, ss5226273542, ss5512026741, ss5661794032, ss5840122552, ss5953228510	NC_000019.9:254898:A:G	NC_000019.10:254898:A:G	(self)
98948551, 531473826, 36989357, 118220385, 280639725, 11204938836, ss3650849044, ss3702151191, ss3820957698, ss3846777696, ss3980611356, ss5065094061, ss5306152318, ss5611422616, ss5784383281, ss5817322606, ss5852168448, ss5926949359	NC_000019.10:254898:A:G	NC_000019.10:254898:A:G	(self)
ss5269992, ss5520287, ss5819563, ss6768373, ss14705871, ss40995080, ss96284283, ss132738411	NT_011255.14:194898:A:G	NC_000019.10:254898: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 rs3861552

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

rs3861552