Name: rs7753489
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.

rs7753489

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr6:49628871 (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>A
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.226786 (60028/264690, TOPMED)
A=0.223682 (31285/139864, GnomAD)
A=0.20493 (5791/28258, 14KJPN) (+ 16 more)
A=0.21202 (4005/18890, ALFA)
A=0.19994 (3351/16760, 8.3KJPN)
A=0.2753 (1763/6404, 1000G_30x)
A=0.2750 (1377/5008, 1000G)
A=0.2020 (905/4480, Estonian)
A=0.1744 (672/3854, ALSPAC)
A=0.1750 (649/3708, TWINSUK)
A=0.2536 (743/2930, KOREAN)
A=0.2675 (490/1832, Korea1K)
A=0.154 (154/998, GoNL)
A=0.167 (100/600, NorthernSweden)
C=0.419 (98/234, SGDP_PRJ)
A=0.255 (55/216, Qatari)
A=0.23 (9/40, GENOME_DK)
C=0.50 (6/12, Siberian)
A=0.50 (6/12, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: RHAG : 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	18890	C=0.78798	A=0.21202
European	Sub	14286	C=0.80981	A=0.19019
African	Sub	2946	C=0.6758	A=0.3242
African Others	Sub	114	C=0.596	A=0.404
African American	Sub	2832	C=0.6790	A=0.3210
Asian	Sub	112	C=0.732	A=0.268
East Asian	Sub	86	C=0.73	A=0.27
Other Asian	Sub	26	C=0.73	A=0.27
Latin American 1	Sub	146	C=0.795	A=0.205
Latin American 2	Sub	610	C=0.841	A=0.159
South Asian	Sub	98	C=0.76	A=0.24
Other	Sub	692	C=0.780	A=0.220

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=0.773214	A=0.226786
gnomAD - Genomes	Global	Study-wide	139864	C=0.776318	A=0.223682
gnomAD - Genomes	European	Sub	75798	C=0.81889	A=0.18111
gnomAD - Genomes	African	Sub	41856	C=0.68427	A=0.31573
gnomAD - Genomes	American	Sub	13624	C=0.83008	A=0.16992
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	C=0.7950	A=0.2050
gnomAD - Genomes	East Asian	Sub	3116	C=0.7202	A=0.2798
gnomAD - Genomes	Other	Sub	2148	C=0.7793	A=0.2207
14KJPN	JAPANESE	Study-wide	28258	C=0.79507	A=0.20493
Allele Frequency Aggregator	Total	Global	18890	C=0.78798	A=0.21202
Allele Frequency Aggregator	European	Sub	14286	C=0.80981	A=0.19019
Allele Frequency Aggregator	African	Sub	2946	C=0.6758	A=0.3242
Allele Frequency Aggregator	Other	Sub	692	C=0.780	A=0.220
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.841	A=0.159
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.795	A=0.205
Allele Frequency Aggregator	Asian	Sub	112	C=0.732	A=0.268
Allele Frequency Aggregator	South Asian	Sub	98	C=0.76	A=0.24
8.3KJPN	JAPANESE	Study-wide	16760	C=0.80006	A=0.19994
1000Genomes_30x	Global	Study-wide	6404	C=0.7247	A=0.2753
1000Genomes_30x	African	Sub	1786	C=0.6265	A=0.3735
1000Genomes_30x	Europe	Sub	1266	C=0.8246	A=0.1754
1000Genomes_30x	South Asian	Sub	1202	C=0.6930	A=0.3070
1000Genomes_30x	East Asian	Sub	1170	C=0.6940	A=0.3060
1000Genomes_30x	American	Sub	980	C=0.850	A=0.150
1000Genomes	Global	Study-wide	5008	C=0.7250	A=0.2750
1000Genomes	African	Sub	1322	C=0.6293	A=0.3707
1000Genomes	East Asian	Sub	1008	C=0.6964	A=0.3036
1000Genomes	Europe	Sub	1006	C=0.8280	A=0.1720
1000Genomes	South Asian	Sub	978	C=0.688	A=0.312
1000Genomes	American	Sub	694	C=0.852	A=0.148
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.7980	A=0.2020
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.8256	A=0.1744
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.8250	A=0.1750
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.7464	A=0.2536
Korean Genome Project	KOREAN	Study-wide	1832	C=0.7325	A=0.2675
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.846	A=0.154
Northern Sweden	ACPOP	Study-wide	600	C=0.833	A=0.167
SGDP_PRJ	Global	Study-wide	234	C=0.419	A=0.581
Qatari	Global	Study-wide	216	C=0.745	A=0.255
The Danish reference pan genome	Danish	Study-wide	40	C=0.78	A=0.23
Siberian	Global	Study-wide	12	C=0.50	A=0.50

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 6	NC_000006.12:g.49628871C>A
GRCh37.p13 chr 6	NC_000006.11:g.49596584C>A
RHAG RefSeqGene (LRG_822)	NG_011704.1:g.13004G>T

Gene: RHAG, Rh associated glycoprotein (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
RHAG transcript	NM_000324.3:c.157+7785G>T	N/A	Intron Variant
RHAG transcript variant X1	XM_011514788.2:c.157+7785… XM_011514788.2:c.157+7785G>T	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=	A
GRCh38.p14 chr 6	NC_000006.12:g.49628871=	NC_000006.12:g.49628871C>A
GRCh37.p13 chr 6	NC_000006.11:g.49596584=	NC_000006.11:g.49596584C>A
RHAG RefSeqGene (LRG_822)	NG_011704.1:g.13004=	NG_011704.1:g.13004G>T
RHAG transcript	NM_000324.2:c.157+7785=	NM_000324.2:c.157+7785G>T
RHAG transcript	NM_000324.3:c.157+7785=	NM_000324.3:c.157+7785G>T
RHAG transcript variant X1	XM_011514788.2:c.157+7785=	XM_011514788.2:c.157+7785G>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#.

50 SubSNP, 18 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	WI_SSAHASNP	ss11798853	Jul 11, 2003 (116)
2	SC_SNP	ss13104912	Dec 05, 2003 (119)
3	BCMHGSC_JDW	ss93457634	Mar 24, 2008 (129)
4	BL	ss254311866	May 09, 2011 (134)
5	GMI	ss278790670	May 04, 2012 (137)
6	1000GENOMES	ss333274308	May 09, 2011 (134)
7	TISHKOFF	ss559198410	Apr 25, 2013 (138)
8	SSMP	ss653141173	Apr 25, 2013 (138)
9	EVA-GONL	ss982920822	Aug 21, 2014 (142)
10	JMKIDD_LAB	ss1073608638	Aug 21, 2014 (142)
11	1000GENOMES	ss1320091137	Aug 21, 2014 (142)
12	DDI	ss1430718565	Apr 01, 2015 (144)
13	EVA_GENOME_DK	ss1581668630	Apr 01, 2015 (144)
14	EVA_DECODE	ss1592457541	Apr 01, 2015 (144)
15	EVA_UK10K_ALSPAC	ss1615559325	Apr 01, 2015 (144)
16	EVA_UK10K_TWINSUK	ss1658553358	Apr 01, 2015 (144)
17	WEILL_CORNELL_DGM	ss1926178076	Feb 12, 2016 (147)
18	JJLAB	ss2023728431	Sep 14, 2016 (149)
19	USC_VALOUEV	ss2151907354	Dec 20, 2016 (150)
20	HUMAN_LONGEVITY	ss2284002139	Dec 20, 2016 (150)
21	SYSTEMSBIOZJU	ss2626351135	Nov 08, 2017 (151)
22	GRF	ss2707507503	Nov 08, 2017 (151)
23	GNOMAD	ss2838885257	Nov 08, 2017 (151)
24	SWEGEN	ss2999046123	Nov 08, 2017 (151)
25	CSHL	ss3346957256	Nov 08, 2017 (151)
26	EGCUT_WGS	ss3666942601	Jul 13, 2019 (153)
27	EVA_DECODE	ss3717189769	Jul 13, 2019 (153)
28	ACPOP	ss3733495597	Jul 13, 2019 (153)
29	EVA	ss3765009777	Jul 13, 2019 (153)
30	KHV_HUMAN_GENOMES	ss3808155128	Jul 13, 2019 (153)
31	EVA	ss3829917968	Apr 26, 2020 (154)
32	EVA	ss3838436852	Apr 26, 2020 (154)
33	EVA	ss3843881717	Apr 26, 2020 (154)
34	SGDP_PRJ	ss3864560368	Apr 26, 2020 (154)
35	KRGDB	ss3911373049	Apr 26, 2020 (154)
36	KOGIC	ss3959013728	Apr 26, 2020 (154)
37	TOPMED	ss4702625777	Apr 26, 2021 (155)
38	TOMMO_GENOMICS	ss5177458043	Apr 26, 2021 (155)
39	1000G_HIGH_COVERAGE	ss5268410528	Oct 13, 2022 (156)
40	EVA	ss5365562082	Oct 13, 2022 (156)
41	HUGCELL_USP	ss5466087063	Oct 13, 2022 (156)
42	EVA	ss5508487879	Oct 13, 2022 (156)
43	1000G_HIGH_COVERAGE	ss5554289398	Oct 13, 2022 (156)
44	SANFORD_IMAGENETICS	ss5640380279	Oct 13, 2022 (156)
45	TOMMO_GENOMICS	ss5715490806	Oct 13, 2022 (156)
46	YY_MCH	ss5807458502	Oct 13, 2022 (156)
47	EVA	ss5842228202	Oct 13, 2022 (156)
48	EVA	ss5855353820	Oct 13, 2022 (156)
49	EVA	ss5883777242	Oct 13, 2022 (156)
50	EVA	ss5968880883	Oct 13, 2022 (156)
51	1000Genomes	NC_000006.11 - 49596584	Oct 12, 2018 (152)
52	1000Genomes_30x	NC_000006.12 - 49628871	Oct 13, 2022 (156)
53	The Avon Longitudinal Study of Parents and Children	NC_000006.11 - 49596584	Oct 12, 2018 (152)
54	Genetic variation in the Estonian population	NC_000006.11 - 49596584	Oct 12, 2018 (152)
55	The Danish reference pan genome	NC_000006.11 - 49596584	Apr 26, 2020 (154)
56	gnomAD - Genomes	NC_000006.12 - 49628871	Apr 26, 2021 (155)
57	Genome of the Netherlands Release 5	NC_000006.11 - 49596584	Apr 26, 2020 (154)
58	KOREAN population from KRGDB	NC_000006.11 - 49596584	Apr 26, 2020 (154)
59	Korean Genome Project	NC_000006.12 - 49628871	Apr 26, 2020 (154)
60	Northern Sweden	NC_000006.11 - 49596584	Jul 13, 2019 (153)
61	Qatari	NC_000006.11 - 49596584	Apr 26, 2020 (154)
62	SGDP_PRJ	NC_000006.11 - 49596584	Apr 26, 2020 (154)
63	Siberian	NC_000006.11 - 49596584	Apr 26, 2020 (154)
64	8.3KJPN	NC_000006.11 - 49596584	Apr 26, 2021 (155)
65	14KJPN	NC_000006.12 - 49628871	Oct 13, 2022 (156)
66	TopMed	NC_000006.12 - 49628871	Apr 26, 2021 (155)
67	UK 10K study - Twins	NC_000006.11 - 49596584	Oct 12, 2018 (152)
68	ALFA	NC_000006.12 - 49628871	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
ss93457634, ss254311866, ss278790670, ss1592457541	NC_000006.10:49704542:C:A	NC_000006.12:49628870:C:A	(self)
31878272, 17777673, 12680849, 7833569, 7910629, 18550443, 6780462, 8220006, 16577348, 4423708, 35427350, 17777673, ss333274308, ss559198410, ss653141173, ss982920822, ss1073608638, ss1320091137, ss1430718565, ss1581668630, ss1615559325, ss1658553358, ss1926178076, ss2023728431, ss2151907354, ss2626351135, ss2707507503, ss2838885257, ss2999046123, ss3346957256, ss3666942601, ss3733495597, ss3765009777, ss3829917968, ss3838436852, ss3864560368, ss3911373049, ss5177458043, ss5365562082, ss5508487879, ss5640380279, ss5842228202, ss5968880883	NC_000006.11:49596583:C:A	NC_000006.12:49628870:C:A	(self)
41815333, 224901244, 15391729, 49327910, 540003335, 9121958999, ss2284002139, ss3717189769, ss3808155128, ss3843881717, ss3959013728, ss4702625777, ss5268410528, ss5466087063, ss5554289398, ss5715490806, ss5807458502, ss5855353820, ss5883777242	NC_000006.12:49628870:C:A	NC_000006.12:49628870:C:A	(self)
ss11798853, ss13104912	NT_007592.13:40393691:C:A	NC_000006.12:49628870:C:A	(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 rs7753489

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
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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

rs7753489