Name: rs10864372
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.

rs10864372

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:8948885 (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 / T>G
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.359009 (95026/264690, TOPMED)
T=0.359415 (49876/138770, GnomAD)
T=0.14265 (4031/28258, 14KJPN) (+ 13 more)
T=0.36216 (6471/17868, ALFA)
T=0.14099 (2363/16760, 8.3KJPN)
T=0.3392 (2172/6404, 1000G_30x)
T=0.3325 (1665/5008, 1000G)
T=0.3897 (1742/4470, Estonian)
T=0.3360 (1295/3854, ALSPAC)
T=0.3376 (1252/3708, TWINSUK)
T=0.1833 (537/2930, KOREAN)
T=0.335 (334/998, GoNL)
T=0.345 (207/600, NorthernSweden)
T=0.197 (94/476, SGDP_PRJ)
T=0.319 (69/216, Qatari)
T=0.30 (13/44, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: CA6 : 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	17868	T=0.36216	A=0.63784, C=0.00000, G=0.00000
European	Sub	13686	T=0.34824	A=0.65176, C=0.00000, G=0.00000
African	Sub	2528	T=0.4399	A=0.5601, C=0.0000, G=0.0000
African Others	Sub	92	T=0.51	A=0.49, C=0.00, G=0.00
African American	Sub	2436	T=0.4372	A=0.5628, C=0.0000, G=0.0000
Asian	Sub	112	T=0.214	A=0.786, C=0.000, G=0.000
East Asian	Sub	86	T=0.17	A=0.83, C=0.00, G=0.00
Other Asian	Sub	26	T=0.35	A=0.65, C=0.00, G=0.00
Latin American 1	Sub	146	T=0.356	A=0.644, C=0.000, G=0.000
Latin American 2	Sub	610	T=0.395	A=0.605, C=0.000, G=0.000
South Asian	Sub	98	T=0.30	A=0.70, C=0.00, G=0.00
Other	Sub	688	T=0.359	A=0.641, C=0.000, G=0.000

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=0.359009	A=0.640991
gnomAD - Genomes	Global	Study-wide	138770	T=0.359415	A=0.640585
gnomAD - Genomes	European	Sub	75348	T=0.33747	A=0.66253
gnomAD - Genomes	African	Sub	41340	T=0.40970	A=0.59030
gnomAD - Genomes	American	Sub	13526	T=0.40293	A=0.59707
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	T=0.2428	A=0.7572
gnomAD - Genomes	East Asian	Sub	3106	T=0.1768	A=0.8232
gnomAD - Genomes	Other	Sub	2130	T=0.3315	A=0.6685
14KJPN	JAPANESE	Study-wide	28258	T=0.14265	A=0.85735
Allele Frequency Aggregator	Total	Global	17868	T=0.36216	A=0.63784, C=0.00000, G=0.00000
Allele Frequency Aggregator	European	Sub	13686	T=0.34824	A=0.65176, C=0.00000, G=0.00000
Allele Frequency Aggregator	African	Sub	2528	T=0.4399	A=0.5601, C=0.0000, G=0.0000
Allele Frequency Aggregator	Other	Sub	688	T=0.359	A=0.641, C=0.000, G=0.000
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.395	A=0.605, C=0.000, G=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.356	A=0.644, C=0.000, G=0.000
Allele Frequency Aggregator	Asian	Sub	112	T=0.214	A=0.786, C=0.000, G=0.000
Allele Frequency Aggregator	South Asian	Sub	98	T=0.30	A=0.70, C=0.00, G=0.00
8.3KJPN	JAPANESE	Study-wide	16760	T=0.14099	A=0.85901
1000Genomes_30x	Global	Study-wide	6404	T=0.3392	A=0.6608
1000Genomes_30x	African	Sub	1786	T=0.4356	A=0.5644
1000Genomes_30x	Europe	Sub	1266	T=0.3104	A=0.6896
1000Genomes_30x	South Asian	Sub	1202	T=0.3186	A=0.6814
1000Genomes_30x	East Asian	Sub	1170	T=0.1906	A=0.8094
1000Genomes_30x	American	Sub	980	T=0.403	A=0.597
1000Genomes	Global	Study-wide	5008	T=0.3325	A=0.6675
1000Genomes	African	Sub	1322	T=0.4425	A=0.5575
1000Genomes	East Asian	Sub	1008	T=0.1855	A=0.8145
1000Genomes	Europe	Sub	1006	T=0.3121	A=0.6879
1000Genomes	South Asian	Sub	978	T=0.308	A=0.692
1000Genomes	American	Sub	694	T=0.401	A=0.599
Genetic variation in the Estonian population	Estonian	Study-wide	4470	T=0.3897	A=0.6103
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.3360	A=0.6640
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.3376	A=0.6624
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.1833	A=0.8167
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.335	A=0.665
Northern Sweden	ACPOP	Study-wide	600	T=0.345	A=0.655
SGDP_PRJ	Global	Study-wide	476	T=0.197	A=0.803
Qatari	Global	Study-wide	216	T=0.319	A=0.681
Siberian	Global	Study-wide	44	T=0.30	A=0.70

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.8948885T>A
GRCh38.p14 chr 1	NC_000001.11:g.8948885T>C
GRCh38.p14 chr 1	NC_000001.11:g.8948885T>G
GRCh37.p13 chr 1	NC_000001.10:g.9008944T>A
GRCh37.p13 chr 1	NC_000001.10:g.9008944T>C
GRCh37.p13 chr 1	NC_000001.10:g.9008944T>G
CA6 RefSeqGene	NG_033975.1:g.8052T>A
CA6 RefSeqGene	NG_033975.1:g.8052T>C
CA6 RefSeqGene	NG_033975.1:g.8052T>G

Gene: CA6, carbonic anhydrase 6 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CA6 transcript variant 1	NM_001215.4:c.80-378T>A	N/A	Intron Variant
CA6 transcript variant 2	NM_001270500.2:c.80-378T>A	N/A	Intron Variant
CA6 transcript variant 3	NM_001270501.2:c.79+2920T… NM_001270501.2:c.79+2920T>A	N/A	Intron Variant
CA6 transcript variant 4	NM_001270502.2:c.24+2920T… NM_001270502.2:c.24+2920T>A	N/A	Intron Variant
CA6 transcript variant X2	XM_011542083.4:c.92-378T>A	N/A	Intron Variant
CA6 transcript variant X1	XM_011542084.4:c.92-378T>A	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	T=	A	C	G
GRCh38.p14 chr 1	NC_000001.11:g.8948885=	NC_000001.11:g.8948885T>A	NC_000001.11:g.8948885T>C	NC_000001.11:g.8948885T>G
GRCh37.p13 chr 1	NC_000001.10:g.9008944=	NC_000001.10:g.9008944T>A	NC_000001.10:g.9008944T>C	NC_000001.10:g.9008944T>G
CA6 RefSeqGene	NG_033975.1:g.8052=	NG_033975.1:g.8052T>A	NG_033975.1:g.8052T>C	NG_033975.1:g.8052T>G
CA6 transcript variant 1	NM_001215.3:c.80-378=	NM_001215.3:c.80-378T>A	NM_001215.3:c.80-378T>C	NM_001215.3:c.80-378T>G
CA6 transcript variant 1	NM_001215.4:c.80-378=	NM_001215.4:c.80-378T>A	NM_001215.4:c.80-378T>C	NM_001215.4:c.80-378T>G
CA6 transcript variant 2	NM_001270500.1:c.80-378=	NM_001270500.1:c.80-378T>A	NM_001270500.1:c.80-378T>C	NM_001270500.1:c.80-378T>G
CA6 transcript variant 2	NM_001270500.2:c.80-378=	NM_001270500.2:c.80-378T>A	NM_001270500.2:c.80-378T>C	NM_001270500.2:c.80-378T>G
CA6 transcript variant 3	NM_001270501.1:c.79+2920=	NM_001270501.1:c.79+2920T>A	NM_001270501.1:c.79+2920T>C	NM_001270501.1:c.79+2920T>G
CA6 transcript variant 3	NM_001270501.2:c.79+2920=	NM_001270501.2:c.79+2920T>A	NM_001270501.2:c.79+2920T>C	NM_001270501.2:c.79+2920T>G
CA6 transcript variant 4	NM_001270502.1:c.24+2920=	NM_001270502.1:c.24+2920T>A	NM_001270502.1:c.24+2920T>C	NM_001270502.1:c.24+2920T>G
CA6 transcript variant 4	NM_001270502.2:c.24+2920=	NM_001270502.2:c.24+2920T>A	NM_001270502.2:c.24+2920T>C	NM_001270502.2:c.24+2920T>G
CA6 transcript variant X2	XM_011542083.4:c.92-378=	XM_011542083.4:c.92-378T>A	XM_011542083.4:c.92-378T>C	XM_011542083.4:c.92-378T>G
CA6 transcript variant X1	XM_011542084.4:c.92-378=	XM_011542084.4:c.92-378T>A	XM_011542084.4:c.92-378T>C	XM_011542084.4:c.92-378T>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#.

60 SubSNP, 16 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss18069716	Feb 27, 2004 (120)
2	SC_SNP	ss18135795	Feb 27, 2004 (120)
3	CSHL-HAPMAP	ss19095315	Feb 27, 2004 (120)
4	SSAHASNP	ss20429398	Apr 05, 2004 (121)
5	ABI	ss41121928	Mar 16, 2006 (126)
6	AFFY	ss76793106	Dec 07, 2007 (131)
7	HUMANGENOME_JCVI	ss97918309	Feb 04, 2009 (130)
8	ENSEMBL	ss131822840	Dec 01, 2009 (131)
9	COMPLETE_GENOMICS	ss163054293	Jul 04, 2010 (132)
10	COMPLETE_GENOMICS	ss163806310	Jul 04, 2010 (132)
11	COMPLETE_GENOMICS	ss166074579	Jul 04, 2010 (132)
12	BUSHMAN	ss197992936	Jul 04, 2010 (132)
13	1000GENOMES	ss218227908	Jul 14, 2010 (132)
14	BL	ss252906073	May 09, 2011 (134)
15	GMI	ss275707557	May 04, 2012 (137)
16	TISHKOFF	ss553777281	Apr 25, 2013 (138)
17	SSMP	ss647564090	Apr 25, 2013 (138)
18	EVA-GONL	ss974838885	Aug 21, 2014 (142)
19	JMKIDD_LAB	ss1067658361	Aug 21, 2014 (142)
20	1000GENOMES	ss1289615748	Aug 21, 2014 (142)
21	DDI	ss1425707208	Apr 01, 2015 (144)
22	EVA_UK10K_ALSPAC	ss1599513822	Apr 01, 2015 (144)
23	EVA_UK10K_TWINSUK	ss1642507855	Apr 01, 2015 (144)
24	EVA_SVP	ss1712310051	Apr 01, 2015 (144)
25	HAMMER_LAB	ss1793872742	Sep 08, 2015 (146)
26	WEILL_CORNELL_DGM	ss1918037351	Feb 12, 2016 (147)
27	JJLAB	ss2019533466	Sep 14, 2016 (149)
28	USC_VALOUEV	ss2147528345	Dec 20, 2016 (150)
29	SYSTEMSBIOZJU	ss2624282690	Nov 08, 2017 (151)
30	GRF	ss2697424777	Nov 08, 2017 (151)
31	GNOMAD	ss2751427609	Nov 08, 2017 (151)
32	SWEGEN	ss2986268197	Nov 08, 2017 (151)
33	BIOINF_KMB_FNS_UNIBA	ss3023531444	Nov 08, 2017 (151)
34	CSHL	ss3343310076	Nov 08, 2017 (151)
35	URBANLAB	ss3646596736	Oct 11, 2018 (152)
36	EGCUT_WGS	ss3654367975	Jul 12, 2019 (153)
37	EVA_DECODE	ss3686129605	Jul 12, 2019 (153)
38	ACPOP	ss3726775408	Jul 12, 2019 (153)
39	EVA	ss3745808391	Jul 12, 2019 (153)
40	PACBIO	ss3783320252	Jul 12, 2019 (153)
41	PACBIO	ss3788995850	Jul 12, 2019 (153)
42	PACBIO	ss3793868581	Jul 12, 2019 (153)
43	KHV_HUMAN_GENOMES	ss3798829094	Jul 12, 2019 (153)
44	EVA	ss3826015469	Apr 25, 2020 (154)
45	EVA	ss3836394960	Apr 25, 2020 (154)
46	EVA	ss3841799400	Apr 25, 2020 (154)
47	SGDP_PRJ	ss3848158452	Apr 25, 2020 (154)
48	KRGDB	ss3893032759	Apr 25, 2020 (154)
49	TOPMED	ss4438658973	Apr 25, 2021 (155)
50	TOMMO_GENOMICS	ss5142391751	Apr 25, 2021 (155)
51	1000G_HIGH_COVERAGE	ss5241114454	Oct 13, 2022 (156)
52	HUGCELL_USP	ss5442324424	Oct 13, 2022 (156)
53	1000G_HIGH_COVERAGE	ss5512846225	Oct 13, 2022 (156)
54	SANFORD_IMAGENETICS	ss5624891791	Oct 13, 2022 (156)
55	TOMMO_GENOMICS	ss5666666310	Oct 13, 2022 (156)
56	YY_MCH	ss5800307972	Oct 13, 2022 (156)
57	EVA	ss5831516862	Oct 13, 2022 (156)
58	EVA	ss5906976967	Oct 13, 2022 (156)
59	EVA	ss5936718339	Oct 13, 2022 (156)
60	EVA	ss5979932024	Oct 13, 2022 (156)
61	1000Genomes	NC_000001.10 - 9008944	Oct 11, 2018 (152)
62	1000Genomes_30x	NC_000001.11 - 8948885	Oct 13, 2022 (156)
63	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 9008944	Oct 11, 2018 (152)
64	Genetic variation in the Estonian population	NC_000001.10 - 9008944	Oct 11, 2018 (152)
65	gnomAD - Genomes	NC_000001.11 - 8948885	Apr 25, 2021 (155)
66	Genome of the Netherlands Release 5	NC_000001.10 - 9008944	Apr 25, 2020 (154)
67	KOREAN population from KRGDB	NC_000001.10 - 9008944	Apr 25, 2020 (154)
68	Northern Sweden	NC_000001.10 - 9008944	Jul 12, 2019 (153)
69	Qatari	NC_000001.10 - 9008944	Apr 25, 2020 (154)
70	SGDP_PRJ	NC_000001.10 - 9008944	Apr 25, 2020 (154)
71	Siberian	NC_000001.10 - 9008944	Apr 25, 2020 (154)
72	8.3KJPN	NC_000001.10 - 9008944	Apr 25, 2021 (155)
73	14KJPN	NC_000001.11 - 8948885	Oct 13, 2022 (156)
74	TopMed	NC_000001.11 - 8948885	Apr 25, 2021 (155)
75	UK 10K study - Twins	NC_000001.10 - 9008944	Oct 11, 2018 (152)
76	ALFA	NC_000001.11 - 8948885	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)
rs36148478	Oct 16, 2006 (127)
rs56125851	Dec 02, 2009 (131)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss76793106, ss163054293, ss163806310, ss166074579, ss197992936, ss252906073, ss275707557, ss1712310051	NC_000001.9:8931530:T:A	NC_000001.11:8948884:T:A	(self)
289358, 148466, 106223, 63825, 210153, 60273, 79281, 175432, 44699, 361058, 148466, ss218227908, ss553777281, ss647564090, ss974838885, ss1067658361, ss1289615748, ss1425707208, ss1599513822, ss1642507855, ss1793872742, ss1918037351, ss2019533466, ss2147528345, ss2624282690, ss2697424777, ss2751427609, ss2986268197, ss3343310076, ss3654367975, ss3726775408, ss3745808391, ss3783320252, ss3788995850, ss3793868581, ss3826015469, ss3836394960, ss3848158452, ss3893032759, ss5142391751, ss5624891791, ss5831516862, ss5936718339, ss5979932024	NC_000001.10:9008943:T:A	NC_000001.11:8948884:T:A	(self)
372160, 2010497, 503414, 2265308, 7036603449, ss3023531444, ss3646596736, ss3686129605, ss3798829094, ss3841799400, ss4438658973, ss5241114454, ss5442324424, ss5512846225, ss5666666310, ss5800307972, ss5906976967	NC_000001.11:8948884:T:A	NC_000001.11:8948884:T:A	(self)
ss18069716, ss18135795, ss19095315, ss20429398	NT_021937.16:3136002:T:A	NC_000001.11:8948884:T:A	(self)
ss41121928, ss97918309, ss131822840	NT_021937.19:5013675:T:A	NC_000001.11:8948884:T:A	(self)
7036603449	NC_000001.11:8948884:T:C	NC_000001.11:8948884:T:C	(self)
7036603449	NC_000001.11:8948884:T:G	NC_000001.11:8948884: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 rs10864372

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

rs10864372