Name: rs11075299
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.

rs11075299

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr16:16152307 (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>G
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.213068 (56397/264690, TOPMED)
G=0.20906 (7762/37128, ALFA)
G=0.16017 (4525/28252, 14KJPN) (+ 13 more)
G=0.15994 (2680/16756, 8.3KJPN)
G=0.1785 (1143/6404, 1000G_30x)
G=0.1795 (899/5008, 1000G)
G=0.3183 (1426/4480, Estonian)
G=0.2867 (1105/3854, ALSPAC)
G=0.2805 (1040/3708, TWINSUK)
G=0.1468 (430/2930, KOREAN)
G=0.286 (285/998, GoNL)
G=0.338 (203/600, NorthernSweden)
G=0.139 (30/216, Qatari)
T=0.406 (65/160, SGDP_PRJ)
G=0.40 (16/40, GENOME_DK)
T=0.45 (10/22, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ABCC6 : 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	37128	T=0.79094	A=0.00000, G=0.20906
European	Sub	26204	T=0.75901	A=0.00000, G=0.24099
African	Sub	5900	T=0.9419	A=0.0000, G=0.0581
African Others	Sub	212	T=0.972	A=0.000, G=0.028
African American	Sub	5688	T=0.9408	A=0.0000, G=0.0592
Asian	Sub	402	T=0.863	A=0.000, G=0.137
East Asian	Sub	340	T=0.859	A=0.000, G=0.141
Other Asian	Sub	62	T=0.89	A=0.00, G=0.11
Latin American 1	Sub	234	T=0.876	A=0.000, G=0.124
Latin American 2	Sub	1054	T=0.8027	A=0.0000, G=0.1973
South Asian	Sub	122	T=0.885	A=0.000, G=0.115
Other	Sub	3212	T=0.7516	A=0.0000, G=0.2484

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	T=0.786932	G=0.213068
Allele Frequency Aggregator	Total	Global	37128	T=0.79094	A=0.00000, G=0.20906
Allele Frequency Aggregator	European	Sub	26204	T=0.75901	A=0.00000, G=0.24099
Allele Frequency Aggregator	African	Sub	5900	T=0.9419	A=0.0000, G=0.0581
Allele Frequency Aggregator	Other	Sub	3212	T=0.7516	A=0.0000, G=0.2484
Allele Frequency Aggregator	Latin American 2	Sub	1054	T=0.8027	A=0.0000, G=0.1973
Allele Frequency Aggregator	Asian	Sub	402	T=0.863	A=0.000, G=0.137
Allele Frequency Aggregator	Latin American 1	Sub	234	T=0.876	A=0.000, G=0.124
Allele Frequency Aggregator	South Asian	Sub	122	T=0.885	A=0.000, G=0.115
14KJPN	JAPANESE	Study-wide	28252	T=0.83983	G=0.16017
8.3KJPN	JAPANESE	Study-wide	16756	T=0.84006	G=0.15994
1000Genomes_30x	Global	Study-wide	6404	T=0.8215	G=0.1785
1000Genomes_30x	African	Sub	1786	T=0.9423	G=0.0577
1000Genomes_30x	Europe	Sub	1266	T=0.7054	G=0.2946
1000Genomes_30x	South Asian	Sub	1202	T=0.8111	G=0.1889
1000Genomes_30x	East Asian	Sub	1170	T=0.8821	G=0.1179
1000Genomes_30x	American	Sub	980	T=0.692	G=0.308
1000Genomes	Global	Study-wide	5008	T=0.8205	G=0.1795
1000Genomes	African	Sub	1322	T=0.9448	G=0.0552
1000Genomes	East Asian	Sub	1008	T=0.8750	G=0.1250
1000Genomes	Europe	Sub	1006	T=0.6978	G=0.3022
1000Genomes	South Asian	Sub	978	T=0.805	G=0.195
1000Genomes	American	Sub	694	T=0.705	G=0.295
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.6817	G=0.3183
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.7133	G=0.2867
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.7195	G=0.2805
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.8532	G=0.1468
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.714	G=0.286
Northern Sweden	ACPOP	Study-wide	600	T=0.662	G=0.338
Qatari	Global	Study-wide	216	T=0.861	G=0.139
SGDP_PRJ	Global	Study-wide	160	T=0.406	G=0.594
The Danish reference pan genome	Danish	Study-wide	40	T=0.60	G=0.40
Siberian	Global	Study-wide	22	T=0.45	G=0.55

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 16	NC_000016.10:g.16152307T>A
GRCh38.p14 chr 16	NC_000016.10:g.16152307T>G
GRCh37.p13 chr 16	NC_000016.9:g.16246164T>A
GRCh37.p13 chr 16	NC_000016.9:g.16246164T>G
ABCC6 RefSeqGene (LRG_1115)	NG_007558.3:g.76311A>T
ABCC6 RefSeqGene (LRG_1115)	NG_007558.3:g.76311A>C
GRCh38.p14 chr 16 alt locus HSCHR16_1_CTG1	NT_187607.1:g.1810235G>T
GRCh38.p14 chr 16 alt locus HSCHR16_1_CTG1	NT_187607.1:g.1810235G>A

Gene: ABCC6, ATP binding cassette subfamily C member 6 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ABCC6 transcript variant 1	NM_001171.6:c.4209-1535A>T	N/A	Intron Variant
ABCC6 transcript variant 3	NM_001351800.1:c.3867-153… NM_001351800.1:c.3867-1535A>T	N/A	Intron Variant
ABCC6 transcript variant 2	NM_001079528.4:c.	N/A	Genic Downstream Transcript Variant
ABCC6 transcript variant 4	NR_147784.1:n.	N/A	Intron Variant
ABCC6 transcript variant X1	XM_011522479.3:c.4176-153… XM_011522479.3:c.4176-1535A>T	N/A	Intron Variant
ABCC6 transcript variant X3	XM_011522480.1:c.3867-153… XM_011522480.1:c.3867-1535A>T	N/A	Intron Variant
ABCC6 transcript variant X4	XM_011522481.4:c.3867-153… XM_011522481.4:c.3867-1535A>T	N/A	Intron Variant
ABCC6 transcript variant X2	XM_017023212.2:c.4041-153… XM_017023212.2:c.4041-1535A>T	N/A	Intron Variant
ABCC6 transcript variant X10	XM_011522482.4:c.	N/A	Genic Downstream Transcript Variant
ABCC6 transcript variant X8	XM_017023214.2:c.	N/A	Genic Downstream Transcript Variant
ABCC6 transcript variant X9	XM_047434069.1:c.	N/A	Genic Downstream Transcript Variant
ABCC6 transcript variant X5	XR_932836.3:n.	N/A	Genic Downstream Transcript Variant
ABCC6 transcript variant X7	XR_932837.4:n.	N/A	Genic Downstream Transcript Variant
ABCC6 transcript variant X6	XR_932838.4: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	G
GRCh38.p14 chr 16	NC_000016.10:g.16152307=	NC_000016.10:g.16152307T>A	NC_000016.10:g.16152307T>G
GRCh37.p13 chr 16	NC_000016.9:g.16246164=	NC_000016.9:g.16246164T>A	NC_000016.9:g.16246164T>G
ABCC6 RefSeqGene (LRG_1115)	NG_007558.3:g.76311=	NG_007558.3:g.76311A>T	NG_007558.3:g.76311A>C
GRCh38.p14 chr 16 alt locus HSCHR16_1_CTG1	NT_187607.1:g.1810235G>T	NT_187607.1:g.1810235G>A	NT_187607.1:g.1810235=
ABCC6 transcript variant 1	NM_001171.5:c.4209-1535=	NM_001171.5:c.4209-1535A>T	NM_001171.5:c.4209-1535A>C
ABCC6 transcript variant 1	NM_001171.6:c.4209-1535=	NM_001171.6:c.4209-1535A>T	NM_001171.6:c.4209-1535A>C
ABCC6 transcript variant 3	NM_001351800.1:c.3867-1535=	NM_001351800.1:c.3867-1535A>T	NM_001351800.1:c.3867-1535A>C
ABCC6 transcript variant X1	XM_011522479.3:c.4176-1535=	XM_011522479.3:c.4176-1535A>T	XM_011522479.3:c.4176-1535A>C
ABCC6 transcript variant X3	XM_011522480.1:c.3867-1535=	XM_011522480.1:c.3867-1535A>T	XM_011522480.1:c.3867-1535A>C
ABCC6 transcript variant X4	XM_011522481.4:c.3867-1535=	XM_011522481.4:c.3867-1535A>T	XM_011522481.4:c.3867-1535A>C
ABCC6 transcript variant X2	XM_017023212.2:c.4041-1535=	XM_017023212.2:c.4041-1535A>T	XM_017023212.2:c.4041-1535A>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#.

74 SubSNP, 18 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	CSHL-HAPMAP	ss16713869	Feb 27, 2004 (120)
2	CSHL-HAPMAP	ss19345358	Feb 27, 2004 (120)
3	ABI	ss43969347	Mar 14, 2006 (126)
4	HGSV	ss78189695	Dec 06, 2007 (129)
5	HUMANGENOME_JCVI	ss96628285	Feb 03, 2009 (130)
6	1000GENOMES	ss109234856	Jan 23, 2009 (130)
7	1000GENOMES	ss114911070	Jan 25, 2009 (130)
8	ENSEMBL	ss132458198	Dec 01, 2009 (131)
9	ILLUMINA	ss152536325	Dec 01, 2009 (131)
10	GMI	ss157152887	Dec 01, 2009 (131)
11	ILLUMINA	ss159102621	Dec 01, 2009 (131)
12	ILLUMINA	ss159845999	Dec 01, 2009 (131)
13	ILLUMINA	ss168870740	Jul 04, 2010 (132)
14	COMPLETE_GENOMICS	ss169308396	Jul 04, 2010 (132)
15	BCM-HGSC-SUB	ss207686563	Jul 04, 2010 (132)
16	1000GENOMES	ss227170893	Jul 14, 2010 (132)
17	1000GENOMES	ss236973258	Jul 15, 2010 (132)
18	1000GENOMES	ss243323805	Jul 15, 2010 (132)
19	BL	ss255552054	May 09, 2011 (134)
20	GMI	ss282457501	May 04, 2012 (137)
21	GMI	ss287043568	Apr 25, 2013 (138)
22	PJP	ss291928878	May 09, 2011 (134)
23	ILLUMINA	ss479154430	Sep 08, 2015 (146)
24	ILLUMINA	ss532727813	Sep 08, 2015 (146)
25	TISHKOFF	ss564815825	Apr 25, 2013 (138)
26	SSMP	ss660561953	Apr 25, 2013 (138)
27	ILLUMINA	ss832615417	Aug 21, 2014 (142)
28	ILLUMINA	ss833206106	Aug 21, 2014 (142)
29	EVA-GONL	ss992337946	Aug 21, 2014 (142)
30	JMKIDD_LAB	ss1080525929	Aug 21, 2014 (142)
31	1000GENOMES	ss1355597779	Aug 21, 2014 (142)
32	DDI	ss1427794551	Apr 01, 2015 (144)
33	EVA_GENOME_DK	ss1577857954	Apr 01, 2015 (144)
34	EVA_UK10K_ALSPAC	ss1634121546	Apr 01, 2015 (144)
35	EVA_UK10K_TWINSUK	ss1677115579	Apr 01, 2015 (144)
36	EVA_DECODE	ss1696373162	Apr 01, 2015 (144)
37	WEILL_CORNELL_DGM	ss1935755502	Feb 12, 2016 (147)
38	GENOMED	ss1968232313	Jul 19, 2016 (147)
39	JJLAB	ss2028664702	Sep 14, 2016 (149)
40	USC_VALOUEV	ss2157076233	Dec 20, 2016 (150)
41	HUMAN_LONGEVITY	ss2211036886	Dec 20, 2016 (150)
42	SYSTEMSBIOZJU	ss2628826500	Nov 08, 2017 (151)
43	GRF	ss2701575189	Nov 08, 2017 (151)
44	SWEGEN	ss3014156639	Nov 08, 2017 (151)
45	BIOINF_KMB_FNS_UNIBA	ss3028157948	Nov 08, 2017 (151)
46	CSHL	ss3351362880	Nov 08, 2017 (151)
47	ILLUMINA	ss3627490017	Oct 12, 2018 (152)
48	ILLUMINA	ss3636325272	Oct 12, 2018 (152)
49	ILLUMINA	ss3638116595	Oct 12, 2018 (152)
50	URBANLAB	ss3650476009	Oct 12, 2018 (152)
51	EGCUT_WGS	ss3681269800	Jul 13, 2019 (153)
52	ACPOP	ss3741382263	Jul 13, 2019 (153)
53	EVA	ss3753751348	Jul 13, 2019 (153)
54	KHV_HUMAN_GENOMES	ss3819045243	Jul 13, 2019 (153)
55	EVA	ss3834501445	Apr 27, 2020 (154)
56	EVA	ss3840856224	Apr 27, 2020 (154)
57	EVA	ss3846347601	Apr 27, 2020 (154)
58	SGDP_PRJ	ss3884057753	Apr 27, 2020 (154)
59	KRGDB	ss3933369364	Apr 27, 2020 (154)
60	VINODS	ss4032512633	Apr 27, 2021 (155)
61	TOPMED	ss5009584113	Apr 27, 2021 (155)
62	TOMMO_GENOMICS	ss5218676483	Apr 27, 2021 (155)
63	1000G_HIGH_COVERAGE	ss5300327327	Oct 17, 2022 (156)
64	EVA	ss5422654527	Oct 17, 2022 (156)
65	HUGCELL_USP	ss5493826724	Oct 17, 2022 (156)
66	EVA	ss5511578614	Oct 17, 2022 (156)
67	1000G_HIGH_COVERAGE	ss5602646039	Oct 17, 2022 (156)
68	SANFORD_IMAGENETICS	ss5658572751	Oct 17, 2022 (156)
69	TOMMO_GENOMICS	ss5773231597	Oct 17, 2022 (156)
70	YY_MCH	ss5815804580	Oct 17, 2022 (156)
71	EVA	ss5846177382	Oct 17, 2022 (156)
72	EVA	ss5851513578	Oct 17, 2022 (156)
73	EVA	ss5898492781	Oct 17, 2022 (156)
74	EVA	ss5950002461	Oct 17, 2022 (156)
75	1000Genomes	NC_000016.9 - 16246164	Oct 12, 2018 (152)
76	1000Genomes_30x	NC_000016.10 - 16152307	Oct 17, 2022 (156)
77	The Avon Longitudinal Study of Parents and Children	NC_000016.9 - 16246164	Oct 12, 2018 (152)
78	Genetic variation in the Estonian population	NC_000016.9 - 16246164	Oct 12, 2018 (152)
79	The Danish reference pan genome	NC_000016.9 - 16246164	Apr 27, 2020 (154)
80	gnomAD - Genomes Submission ignored due to conflicting rows: Row 484390044 (NC_000016.10:16152306:T:A 2/139250) Row 484390045 (NC_000016.10:16152306:T:G 31529/139184)	-	Apr 27, 2021 (155)
81	gnomAD - Genomes Submission ignored due to conflicting rows: Row 484390044 (NC_000016.10:16152306:T:A 2/139250) Row 484390045 (NC_000016.10:16152306:T:G 31529/139184)	-	Apr 27, 2021 (155)
82	Genome of the Netherlands Release 5	NC_000016.9 - 16246164	Apr 27, 2020 (154)
83	KOREAN population from KRGDB	NC_000016.9 - 16246164	Apr 27, 2020 (154)
84	Northern Sweden	NC_000016.9 - 16246164	Jul 13, 2019 (153)
85	Qatari	NC_000016.9 - 16246164	Apr 27, 2020 (154)
86	SGDP_PRJ	NC_000016.9 - 16246164	Apr 27, 2020 (154)
87	Siberian	NC_000016.9 - 16246164	Apr 27, 2020 (154)
88	8.3KJPN	NC_000016.9 - 16246164	Apr 27, 2021 (155)
89	14KJPN	NC_000016.10 - 16152307	Oct 17, 2022 (156)
90	TopMed	NC_000016.10 - 16152307	Apr 27, 2021 (155)
91	UK 10K study - Twins	NC_000016.9 - 16246164	Oct 12, 2018 (152)
92	ALFA	NC_000016.10 - 16152307	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
10384507450	NC_000016.10:16152306:T:A	NC_000016.10:16152306:T:A	(self)
ss78189695, ss109234856, ss114911070, ss159845999, ss169308396, ss207686563, ss255552054, ss282457501, ss287043568, ss291928878, ss1696373162	NC_000016.8:16153664:T:G	NC_000016.10:16152306:T:G	(self)
68739476, 38166427, 27008048, 4072657, 17024996, 40546758, 14667128, 17797424, 36074733, 9592587, 76645790, 38166427, ss227170893, ss236973258, ss243323805, ss479154430, ss532727813, ss564815825, ss660561953, ss832615417, ss833206106, ss992337946, ss1080525929, ss1355597779, ss1427794551, ss1577857954, ss1634121546, ss1677115579, ss1935755502, ss1968232313, ss2028664702, ss2157076233, ss2628826500, ss2701575189, ss3014156639, ss3351362880, ss3627490017, ss3636325272, ss3638116595, ss3681269800, ss3741382263, ss3753751348, ss3834501445, ss3840856224, ss3884057753, ss3933369364, ss5218676483, ss5422654527, ss5511578614, ss5658572751, ss5846177382, ss5950002461	NC_000016.9:16246163:T:G	NC_000016.10:16152306:T:G	(self)
90171974, 107068701, 225129774, 10384507450, ss2211036886, ss3028157948, ss3650476009, ss3819045243, ss3846347601, ss5009584113, ss5300327327, ss5493826724, ss5602646039, ss5773231597, ss5815804580, ss5851513578, ss5898492781	NC_000016.10:16152306:T:G	NC_000016.10:16152306:T:G	(self)
ss16713869, ss19345358	NT_010393.14:7558297:T:G	NC_000016.10:16152306:T:G	(self)
ss43969347, ss96628285, ss132458198, ss152536325, ss157152887, ss159102621, ss168870740	NT_010393.16:16186163:T:G	NC_000016.10:16152306:T:G	(self)
ss4032512633	NT_187607.1:1810234:G:G	NC_000016.10:16152306:T: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 rs11075299

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

rs11075299