Name: rs11955175
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.

rs11955175

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr5:40626651 (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: T>A / T>C
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.078322 (20731/264690, TOPMED)
C=0.06947 (5467/78694, PAGE_STUDY)
C=0.06018 (3403/56546, ALFA) (+ 18 more)
C=0.00007 (2/28258, 14KJPN)
C=0.0604 (387/6404, 1000G_30x)
C=0.0591 (296/5008, 1000G)
C=0.0942 (422/4480, Estonian)
C=0.0659 (254/3854, ALSPAC)
C=0.0655 (243/3708, TWINSUK)
C=0.0014 (4/2922, KOREAN)
C=0.0011 (2/1832, Korea1K)
C=0.0635 (99/1558, HapMap)
C=0.001 (1/792, PRJEB37584)
C=0.026 (16/626, Chileans)
C=0.117 (70/600, NorthernSweden)
C=0.032 (7/216, Qatari)
C=0.10 (8/84, Ancient Sardinia)
T=0.48 (22/46, SGDP_PRJ)
C=0.05 (2/40, GENOME_DK)
T=0.5 (2/4, Siberian)
C=0.5 (2/4, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LOC105374737 : 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	56546	T=0.93982	A=0.00000, C=0.06018
European	Sub	39312	T=0.93763	A=0.00000, C=0.06237
African	Sub	6608	T=0.9242	A=0.0000, C=0.0758
African Others	Sub	208	T=0.923	A=0.000, C=0.077
African American	Sub	6400	T=0.9242	A=0.0000, C=0.0758
Asian	Sub	530	T=1.000	A=0.000, C=0.000
East Asian	Sub	430	T=1.000	A=0.000, C=0.000
Other Asian	Sub	100	T=1.00	A=0.00, C=0.00
Latin American 1	Sub	646	T=0.954	A=0.000, C=0.046
Latin American 2	Sub	5072	T=0.9687	A=0.0000, C=0.0313
South Asian	Sub	172	T=0.983	A=0.000, C=0.017
Other	Sub	4206	T=0.9387	A=0.0000, C=0.0613

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").

Download

Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	T=0.921678	C=0.078322
The PAGE Study	Global	Study-wide	78694	T=0.93053	C=0.06947
The PAGE Study	AfricanAmerican	Sub	32510	T=0.88656	C=0.11344
The PAGE Study	Mexican	Sub	10810	T=0.96457	C=0.03543
The PAGE Study	Asian	Sub	8318	T=0.9993	C=0.0007
The PAGE Study	PuertoRican	Sub	7918	T=0.9492	C=0.0508
The PAGE Study	NativeHawaiian	Sub	4534	T=0.9801	C=0.0199
The PAGE Study	Cuban	Sub	4230	T=0.9480	C=0.0520
The PAGE Study	Dominican	Sub	3826	T=0.9106	C=0.0894
The PAGE Study	CentralAmerican	Sub	2450	T=0.9355	C=0.0645
The PAGE Study	SouthAmerican	Sub	1982	T=0.9566	C=0.0434
The PAGE Study	NativeAmerican	Sub	1260	T=0.9429	C=0.0571
The PAGE Study	SouthAsian	Sub	856	T=0.977	C=0.023
Allele Frequency Aggregator	Total	Global	56546	T=0.93982	A=0.00000, C=0.06018
Allele Frequency Aggregator	European	Sub	39312	T=0.93763	A=0.00000, C=0.06237
Allele Frequency Aggregator	African	Sub	6608	T=0.9242	A=0.0000, C=0.0758
Allele Frequency Aggregator	Latin American 2	Sub	5072	T=0.9687	A=0.0000, C=0.0313
Allele Frequency Aggregator	Other	Sub	4206	T=0.9387	A=0.0000, C=0.0613
Allele Frequency Aggregator	Latin American 1	Sub	646	T=0.954	A=0.000, C=0.046
Allele Frequency Aggregator	Asian	Sub	530	T=1.000	A=0.000, C=0.000
Allele Frequency Aggregator	South Asian	Sub	172	T=0.983	A=0.000, C=0.017
14KJPN	JAPANESE	Study-wide	28258	T=0.99993	C=0.00007
1000Genomes_30x	Global	Study-wide	6404	T=0.9396	C=0.0604
1000Genomes_30x	African	Sub	1786	T=0.8813	C=0.1187
1000Genomes_30x	Europe	Sub	1266	T=0.9352	C=0.0648
1000Genomes_30x	South Asian	Sub	1202	T=0.9667	C=0.0333
1000Genomes_30x	East Asian	Sub	1170	T=1.0000	C=0.0000
1000Genomes_30x	American	Sub	980	T=0.946	C=0.054
1000Genomes	Global	Study-wide	5008	T=0.9409	C=0.0591
1000Genomes	African	Sub	1322	T=0.8812	C=0.1188
1000Genomes	East Asian	Sub	1008	T=1.0000	C=0.0000
1000Genomes	Europe	Sub	1006	T=0.9314	C=0.0686
1000Genomes	South Asian	Sub	978	T=0.963	C=0.037
1000Genomes	American	Sub	694	T=0.951	C=0.049
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.9058	C=0.0942
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.9341	C=0.0659
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.9345	C=0.0655
KOREAN population from KRGDB	KOREAN	Study-wide	2922	T=0.9986	C=0.0014
Korean Genome Project	KOREAN	Study-wide	1832	T=0.9989	C=0.0011
HapMap	Global	Study-wide	1558	T=0.9365	C=0.0635
HapMap	African	Sub	692	T=0.918	C=0.082
HapMap	American	Sub	600	T=0.943	C=0.057
HapMap	Europe	Sub	176	T=0.955	C=0.045
HapMap	Asian	Sub	90	T=1.00	C=0.00
CNV burdens in cranial meningiomas	Global	Study-wide	792	T=0.999	C=0.001
CNV burdens in cranial meningiomas	CRM	Sub	792	T=0.999	C=0.001
Chileans	Chilean	Study-wide	626	T=0.974	C=0.026
Northern Sweden	ACPOP	Study-wide	600	T=0.883	C=0.117
Qatari	Global	Study-wide	216	T=0.968	C=0.032
Ancient Sardinia genome-wide 1240k capture data generation and analysis	Global	Study-wide	84	T=0.90	C=0.10
SGDP_PRJ	Global	Study-wide	46	T=0.48	C=0.52
The Danish reference pan genome	Danish	Study-wide	40	T=0.95	C=0.05
Siberian	Global	Study-wide	4	T=0.5	C=0.5

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 5	NC_000005.10:g.40626651T>A
GRCh38.p14 chr 5	NC_000005.10:g.40626651T>C
GRCh37.p13 chr 5	NC_000005.9:g.40626753T>A
GRCh37.p13 chr 5	NC_000005.9:g.40626753T>C

Gene: LOC105374737, uncharacterized LOC105374737 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105374737 transcript variant X1	XR_925942.3:n.	N/A	Intron Variant
LOC105374737 transcript variant X2	XR_007058745.1:n.	N/A	Genic Downstream Transcript 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	T=	A	C
GRCh38.p14 chr 5	NC_000005.10:g.40626651=	NC_000005.10:g.40626651T>A	NC_000005.10:g.40626651T>C
GRCh37.p13 chr 5	NC_000005.9:g.40626753=	NC_000005.9:g.40626753T>A	NC_000005.9:g.40626753T>C

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#.

69 SubSNP, 22 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	CSHL-HAPMAP	ss17850165	Feb 28, 2004 (120)
2	ABI	ss42586309	Mar 15, 2006 (126)
3	PERLEGEN	ss68933406	May 17, 2007 (127)
4	ILLUMINA	ss75106097	Dec 07, 2007 (129)
5	AFFY	ss76438806	Dec 07, 2007 (129)
6	1000GENOMES	ss111745032	Jan 25, 2009 (130)
7	KRIBB_YJKIM	ss119734811	Dec 01, 2009 (131)
8	ILLUMINA	ss160020603	Dec 01, 2009 (131)
9	COMPLETE_GENOMICS	ss164789277	Jul 04, 2010 (132)
10	ILLUMINA	ss171747199	Jul 04, 2010 (132)
11	BCM-HGSC-SUB	ss207153287	Jul 04, 2010 (132)
12	1000GENOMES	ss221642005	Jul 14, 2010 (132)
13	1000GENOMES	ss232917592	Jul 14, 2010 (132)
14	GMI	ss285162692	Apr 25, 2013 (138)
15	ILLUMINA	ss480148254	Sep 08, 2015 (146)
16	ILLUMINA	ss536740676	Sep 08, 2015 (146)
17	TISHKOFF	ss558346568	Apr 25, 2013 (138)
18	JMKIDD_LAB	ss1072568908	Aug 21, 2014 (142)
19	1000GENOMES	ss1314771083	Aug 21, 2014 (142)
20	EVA_GENOME_DK	ss1581107161	Apr 01, 2015 (144)
21	EVA_DECODE	ss1591003937	Apr 01, 2015 (144)
22	EVA_UK10K_ALSPAC	ss1612723501	Apr 01, 2015 (144)
23	EVA_UK10K_TWINSUK	ss1655717534	Apr 01, 2015 (144)
24	EVA_SVP	ss1712759471	Apr 01, 2015 (144)
25	WEILL_CORNELL_DGM	ss1924743018	Feb 12, 2016 (147)
26	ILLUMINA	ss1958782938	Feb 12, 2016 (147)
27	JJLAB	ss2022975069	Sep 14, 2016 (149)
28	ILLUMINA	ss2094939473	Dec 20, 2016 (150)
29	ILLUMINA	ss2095155982	Dec 20, 2016 (150)
30	USC_VALOUEV	ss2151126429	Dec 20, 2016 (150)
31	HUMAN_LONGEVITY	ss2273132632	Dec 20, 2016 (150)
32	ILLUMINA	ss2635143062	Nov 08, 2017 (151)
33	GNOMAD	ss2823620881	Nov 08, 2017 (151)
34	AFFY	ss2985951007	Nov 08, 2017 (151)
35	SWEGEN	ss2996791226	Nov 08, 2017 (151)
36	ILLUMINA	ss3022483850	Nov 08, 2017 (151)
37	CSHL	ss3346350848	Nov 08, 2017 (151)
38	ILLUMINA	ss3629221643	Oct 12, 2018 (152)
39	ILLUMINA	ss3636709966	Oct 12, 2018 (152)
40	ILLUMINA	ss3638549806	Oct 12, 2018 (152)
41	ILLUMINA	ss3643496080	Oct 12, 2018 (152)
42	BIOINF_KMB_FNS_UNIBA	ss3645873559	Oct 12, 2018 (152)
43	ILLUMINA	ss3652979090	Oct 12, 2018 (152)
44	ILLUMINA	ss3652979091	Oct 12, 2018 (152)
45	EGCUT_WGS	ss3664687141	Jul 13, 2019 (153)
46	EVA_DECODE	ss3714531303	Jul 13, 2019 (153)
47	ILLUMINA	ss3726228522	Jul 13, 2019 (153)
48	ACPOP	ss3732286640	Jul 13, 2019 (153)
49	EVA	ss3763334251	Jul 13, 2019 (153)
50	PAGE_CC	ss3771198527	Jul 13, 2019 (153)
51	KHV_HUMAN_GENOMES	ss3806509935	Jul 13, 2019 (153)
52	EVA	ss3829209558	Apr 26, 2020 (154)
53	SGDP_PRJ	ss3861682777	Apr 26, 2020 (154)
54	KRGDB	ss3908163065	Apr 26, 2020 (154)
55	KOGIC	ss3956489991	Apr 26, 2020 (154)
56	EVA	ss3984546087	Apr 26, 2021 (155)
57	EVA	ss3985137255	Apr 26, 2021 (155)
58	TOPMED	ss4657048659	Apr 26, 2021 (155)
59	1000G_HIGH_COVERAGE	ss5263651688	Oct 13, 2022 (156)
60	EVA	ss5357042592	Oct 13, 2022 (156)
61	HUGCELL_USP	ss5461908735	Oct 13, 2022 (156)
62	EVA	ss5507992769	Oct 13, 2022 (156)
63	1000G_HIGH_COVERAGE	ss5547116149	Oct 13, 2022 (156)
64	SANFORD_IMAGENETICS	ss5624587678	Oct 13, 2022 (156)
65	SANFORD_IMAGENETICS	ss5637640301	Oct 13, 2022 (156)
66	TOMMO_GENOMICS	ss5707303402	Oct 13, 2022 (156)
67	EVA	ss5834821444	Oct 13, 2022 (156)
68	EVA	ss5893861329	Oct 13, 2022 (156)
69	EVA	ss5966059420	Oct 13, 2022 (156)
70	1000Genomes	NC_000005.9 - 40626753	Oct 12, 2018 (152)
71	1000Genomes_30x	NC_000005.10 - 40626651	Oct 13, 2022 (156)
72	The Avon Longitudinal Study of Parents and Children	NC_000005.9 - 40626753	Oct 12, 2018 (152)
73	Chileans	NC_000005.9 - 40626753	Apr 26, 2020 (154)
74	Genetic variation in the Estonian population	NC_000005.9 - 40626753	Oct 12, 2018 (152)
75	The Danish reference pan genome	NC_000005.9 - 40626753	Apr 26, 2020 (154)
76	gnomAD - Genomes Submission ignored due to conflicting rows: Row 186202799 (NC_000005.10:40626650:T:A 4/140116) Row 186202800 (NC_000005.10:40626650:T:C 12212/140090)	-	Apr 26, 2021 (155)
77	gnomAD - Genomes Submission ignored due to conflicting rows: Row 186202799 (NC_000005.10:40626650:T:A 4/140116) Row 186202800 (NC_000005.10:40626650:T:C 12212/140090)	-	Apr 26, 2021 (155)
78	HapMap	NC_000005.10 - 40626651	Apr 26, 2020 (154)
79	KOREAN population from KRGDB	NC_000005.9 - 40626753	Apr 26, 2020 (154)
80	Korean Genome Project	NC_000005.10 - 40626651	Apr 26, 2020 (154)
81	Northern Sweden	NC_000005.9 - 40626753	Jul 13, 2019 (153)
82	The PAGE Study	NC_000005.10 - 40626651	Jul 13, 2019 (153)
83	Ancient Sardinia genome-wide 1240k capture data generation and analysis	NC_000005.9 - 40626753	Apr 26, 2021 (155)
84	CNV burdens in cranial meningiomas	NC_000005.9 - 40626753	Apr 26, 2021 (155)
85	Qatari	NC_000005.9 - 40626753	Apr 26, 2020 (154)
86	SGDP_PRJ	NC_000005.9 - 40626753	Apr 26, 2020 (154)
87	Siberian	NC_000005.9 - 40626753	Apr 26, 2020 (154)
88	14KJPN	NC_000005.10 - 40626651	Oct 13, 2022 (156)
89	TopMed	NC_000005.10 - 40626651	Apr 26, 2021 (155)
90	UK 10K study - Twins	NC_000005.9 - 40626753	Oct 12, 2018 (152)
91	ALFA	NC_000005.10 - 40626651	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
10501353528, ss2273132632	NC_000005.10:40626650:T:A	NC_000005.10:40626650:T:A	(self)
ss76438806, ss111745032, ss160020603, ss164789277, ss207153287, ss285162692, ss1591003937, ss1712759471, ss2094939473, ss2635143062, ss3643496080	NC_000005.8:40662509:T:C	NC_000005.10:40626650:T:C	(self)
26360027, 14660532, 344477, 10425389, 7272100, 15340459, 5571505, 363182, 95452, 6784948, 13699757, 3642783, 14660532, ss221642005, ss232917592, ss480148254, ss536740676, ss558346568, ss1072568908, ss1314771083, ss1581107161, ss1612723501, ss1655717534, ss1924743018, ss1958782938, ss2022975069, ss2095155982, ss2151126429, ss2823620881, ss2985951007, ss2996791226, ss3022483850, ss3346350848, ss3629221643, ss3636709966, ss3638549806, ss3652979090, ss3652979091, ss3664687141, ss3732286640, ss3763334251, ss3829209558, ss3861682777, ss3908163065, ss3984546087, ss3985137255, ss5357042592, ss5507992769, ss5624587678, ss5637640301, ss5834821444, ss5966059420	NC_000005.9:40626752:T:C	NC_000005.10:40626650:T:C	(self)
34642084, 2853463, 12867992, 419996, 41140506, 494426216, 10501353528, ss2273132632, ss3645873559, ss3714531303, ss3726228522, ss3771198527, ss3806509935, ss3956489991, ss4657048659, ss5263651688, ss5461908735, ss5547116149, ss5707303402, ss5893861329	NC_000005.10:40626650:T:C	NC_000005.10:40626650:T:C	(self)
ss17850165	NT_006576.14:23078858:T:C	NC_000005.10:40626650:T:C	(self)
ss42586309, ss68933406, ss75106097, ss119734811, ss171747199	NT_006576.16:40616752:T:C	NC_000005.10:40626650:T:C	(self)

Removed from this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Destination RSIDs
ss2441186916	NC_000005.9:40626752:T:A	NC_000005.10:40626650:T:A

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs11955175

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

rs11955175