Name: rs596430
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.

rs596430

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr11:133922126 (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>C
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.221229 (58557/264690, TOPMED)
T=0.210034 (29411/140030, GnomAD)
T=0.09420 (2662/28258, 14KJPN) (+ 18 more)
T=0.17804 (3429/19260, ALFA)
T=0.09483 (1589/16756, 8.3KJPN)
T=0.1905 (1258/6604, GO-ESP)
T=0.2203 (1411/6404, 1000G_30x)
T=0.2192 (1098/5008, 1000G)
T=0.1313 (588/4480, Estonian)
T=0.1492 (575/3854, ALSPAC)
T=0.1613 (598/3708, TWINSUK)
T=0.0932 (273/2930, KOREAN)
T=0.1103 (202/1832, Korea1K)
T=0.133 (133/998, GoNL)
T=0.112 (67/600, NorthernSweden)
T=0.163 (87/534, MGP)
T=0.167 (89/534, SGDP_PRJ)
T=0.181 (39/216, Qatari)
T=0.203 (43/212, Vietnamese)
T=0.11 (6/54, Siberian)
T=0.12 (5/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: IGSF9B : 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	19260	T=0.17804	C=0.82196
European	Sub	14336	T=0.14230	C=0.85770
African	Sub	2984	T=0.3234	C=0.6766
African Others	Sub	114	T=0.377	C=0.623
African American	Sub	2870	T=0.3213	C=0.6787
Asian	Sub	116	T=0.172	C=0.828
East Asian	Sub	88	T=0.17	C=0.83
Other Asian	Sub	28	T=0.18	C=0.82
Latin American 1	Sub	152	T=0.197	C=0.803
Latin American 2	Sub	616	T=0.248	C=0.752
South Asian	Sub	98	T=0.18	C=0.82
Other	Sub	958	T=0.212	C=0.788

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=0.221229	C=0.778771
gnomAD - Genomes	Global	Study-wide	140030	T=0.210034	C=0.789966
gnomAD - Genomes	European	Sub	75902	T=0.14661	C=0.85339
gnomAD - Genomes	African	Sub	41882	T=0.32322	C=0.67678
gnomAD - Genomes	American	Sub	13650	T=0.25114	C=0.74886
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	T=0.1445	C=0.8555
gnomAD - Genomes	East Asian	Sub	3126	T=0.1388	C=0.8612
gnomAD - Genomes	Other	Sub	2148	T=0.1881	C=0.8119
14KJPN	JAPANESE	Study-wide	28258	T=0.09420	C=0.90580
Allele Frequency Aggregator	Total	Global	19260	T=0.17804	C=0.82196
Allele Frequency Aggregator	European	Sub	14336	T=0.14230	C=0.85770
Allele Frequency Aggregator	African	Sub	2984	T=0.3234	C=0.6766
Allele Frequency Aggregator	Other	Sub	958	T=0.212	C=0.788
Allele Frequency Aggregator	Latin American 2	Sub	616	T=0.248	C=0.752
Allele Frequency Aggregator	Latin American 1	Sub	152	T=0.197	C=0.803
Allele Frequency Aggregator	Asian	Sub	116	T=0.172	C=0.828
Allele Frequency Aggregator	South Asian	Sub	98	T=0.18	C=0.82
8.3KJPN	JAPANESE	Study-wide	16756	T=0.09483	C=0.90517
GO Exome Sequencing Project	Global	Study-wide	6604	T=0.1905	C=0.8095
GO Exome Sequencing Project	European American	Sub	4354	T=0.1429	C=0.8571
GO Exome Sequencing Project	African American	Sub	2250	T=0.2827	C=0.7173
1000Genomes_30x	Global	Study-wide	6404	T=0.2203	C=0.7797
1000Genomes_30x	African	Sub	1786	T=0.3242	C=0.6758
1000Genomes_30x	Europe	Sub	1266	T=0.1627	C=0.8373
1000Genomes_30x	South Asian	Sub	1202	T=0.1930	C=0.8070
1000Genomes_30x	East Asian	Sub	1170	T=0.1350	C=0.8650
1000Genomes_30x	American	Sub	980	T=0.241	C=0.759
1000Genomes	Global	Study-wide	5008	T=0.2192	C=0.7808
1000Genomes	African	Sub	1322	T=0.3313	C=0.6687
1000Genomes	East Asian	Sub	1008	T=0.1349	C=0.8651
1000Genomes	Europe	Sub	1006	T=0.1620	C=0.8380
1000Genomes	South Asian	Sub	978	T=0.190	C=0.810
1000Genomes	American	Sub	694	T=0.252	C=0.748
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.1313	C=0.8688
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.1492	C=0.8508
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.1613	C=0.8387
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.0932	C=0.9068
Korean Genome Project	KOREAN	Study-wide	1832	T=0.1103	C=0.8897
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.133	C=0.867
Northern Sweden	ACPOP	Study-wide	600	T=0.112	C=0.888
Medical Genome Project healthy controls from Spanish population	Spanish controls	Study-wide	534	T=0.163	C=0.837
SGDP_PRJ	Global	Study-wide	534	T=0.167	C=0.833
Qatari	Global	Study-wide	216	T=0.181	C=0.819
A Vietnamese Genetic Variation Database	Global	Study-wide	212	T=0.203	C=0.797
Siberian	Global	Study-wide	54	T=0.11	C=0.89
The Danish reference pan genome	Danish	Study-wide	40	T=0.12	C=0.88

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 11	NC_000011.10:g.133922126T>C
GRCh37.p13 chr 11	NC_000011.9:g.133792021T>C

Gene: IGSF9B, immunoglobulin superfamily member 9B (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
IGSF9B transcript	NM_001277285.4:c.2327+51A… NM_001277285.4:c.2327+51A>G	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=	C
GRCh38.p14 chr 11	NC_000011.10:g.133922126=	NC_000011.10:g.133922126T>C
GRCh37.p13 chr 11	NC_000011.9:g.133792021=	NC_000011.9:g.133792021T>C
IGSF9B transcript	NM_001277285.1:c.2327+51=	NM_001277285.1:c.2327+51A>G
IGSF9B transcript	NM_001277285.4:c.2327+51=	NM_001277285.4:c.2327+51A>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#.

93 SubSNP, 21 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss768302	Aug 11, 2000 (83)
2	WI_SSAHASNP	ss6829457	Feb 20, 2003 (123)
3	SC_SNP	ss16144243	Feb 27, 2004 (123)
4	CSHL-HAPMAP	ss19194625	Feb 27, 2004 (123)
5	SSAHASNP	ss20799857	Apr 05, 2004 (123)
6	HGSV	ss77307522	Dec 06, 2007 (129)
7	HGSV	ss84968440	Dec 15, 2007 (130)
8	BCMHGSC_JDW	ss88896218	Mar 24, 2008 (129)
9	HUMANGENOME_JCVI	ss97429046	Feb 05, 2009 (130)
10	BGI	ss106780551	Feb 05, 2009 (130)
11	1000GENOMES	ss111330673	Jan 25, 2009 (130)
12	1000GENOMES	ss115408046	Jan 25, 2009 (130)
13	ILLUMINA-UK	ss119989420	Dec 01, 2009 (131)
14	ENSEMBL	ss132941820	Dec 01, 2009 (131)
15	GMI	ss156983295	Dec 01, 2009 (131)
16	COMPLETE_GENOMICS	ss168816864	Jul 04, 2010 (132)
17	COMPLETE_GENOMICS	ss171232656	Jul 04, 2010 (132)
18	COMPLETE_GENOMICS	ss175322567	Jul 04, 2010 (132)
19	BUSHMAN	ss203422465	Jul 04, 2010 (132)
20	BCM-HGSC-SUB	ss207925605	Jul 04, 2010 (132)
21	1000GENOMES	ss225554939	Jul 14, 2010 (132)
22	1000GENOMES	ss235785335	Jul 15, 2010 (132)
23	1000GENOMES	ss242371710	Jul 15, 2010 (132)
24	BL	ss255417874	May 09, 2011 (134)
25	GMI	ss281234745	May 04, 2012 (137)
26	GMI	ss286487004	Apr 25, 2013 (138)
27	PJP	ss291174296	May 09, 2011 (134)
28	ILLUMINA	ss535425493	Sep 08, 2015 (146)
29	TISHKOFF	ss562933309	Apr 25, 2013 (138)
30	SSMP	ss658456711	Apr 25, 2013 (138)
31	NHLBI-ESP	ss713060596	Apr 25, 2013 (138)
32	EVA-GONL	ss989138391	Aug 21, 2014 (142)
33	JMKIDD_LAB	ss1078176673	Aug 21, 2014 (142)
34	1000GENOMES	ss1343630430	Aug 21, 2014 (142)
35	DDI	ss1426812296	Apr 01, 2015 (144)
36	EVA_GENOME_DK	ss1576055521	Apr 01, 2015 (144)
37	EVA_DECODE	ss1598809475	Apr 01, 2015 (144)
38	EVA_UK10K_ALSPAC	ss1627825657	Apr 01, 2015 (144)
39	EVA_UK10K_TWINSUK	ss1670819690	Apr 01, 2015 (144)
40	EVA_MGP	ss1711315034	Apr 01, 2015 (144)
41	HAMMER_LAB	ss1807074462	Sep 08, 2015 (146)
42	WEILL_CORNELL_DGM	ss1932496089	Feb 12, 2016 (147)
43	JJLAB	ss2026995841	Sep 14, 2016 (149)
44	USC_VALOUEV	ss2155313049	Dec 20, 2016 (150)
45	HUMAN_LONGEVITY	ss2187070350	Dec 20, 2016 (150)
46	SYSTEMSBIOZJU	ss2627974324	Nov 08, 2017 (151)
47	GRF	ss2699629322	Nov 08, 2017 (151)
48	GNOMAD	ss2906294115	Nov 08, 2017 (151)
49	SWEGEN	ss3009045542	Nov 08, 2017 (151)
50	BIOINF_KMB_FNS_UNIBA	ss3027300402	Nov 08, 2017 (151)
51	CSHL	ss3349872720	Nov 08, 2017 (151)
52	ILLUMINA	ss3626791550	Oct 12, 2018 (152)
53	OMUKHERJEE_ADBS	ss3646435141	Oct 12, 2018 (152)
54	URBANLAB	ss3649741137	Oct 12, 2018 (152)
55	EGCUT_WGS	ss3676380062	Jul 13, 2019 (153)
56	EVA_DECODE	ss3692924948	Jul 13, 2019 (153)
57	ACPOP	ss3738685124	Jul 13, 2019 (153)
58	EVA	ss3750021925	Jul 13, 2019 (153)
59	PACBIO	ss3787112677	Jul 13, 2019 (153)
60	PACBIO	ss3792230399	Jul 13, 2019 (153)
61	PACBIO	ss3797113008	Jul 13, 2019 (153)
62	KHV_HUMAN_GENOMES	ss3815342212	Jul 13, 2019 (153)
63	EVA	ss3824689992	Apr 26, 2020 (154)
64	EVA	ss3825813551	Apr 26, 2020 (154)
65	EVA	ss3832923384	Apr 26, 2020 (154)
66	EVA	ss3840024760	Apr 26, 2020 (154)
67	EVA	ss3845507510	Apr 26, 2020 (154)
68	SGDP_PRJ	ss3877481487	Apr 26, 2020 (154)
69	KRGDB	ss3925968419	Apr 26, 2020 (154)
70	KOGIC	ss3971087919	Apr 26, 2020 (154)
71	FSA-LAB	ss3984017731	Apr 26, 2021 (155)
72	EVA	ss3986552746	Apr 26, 2021 (155)
73	TOPMED	ss4905626558	Apr 26, 2021 (155)
74	TOMMO_GENOMICS	ss5204627807	Apr 26, 2021 (155)
75	EVA	ss5237217618	Apr 26, 2021 (155)
76	1000G_HIGH_COVERAGE	ss5289475136	Oct 13, 2022 (156)
77	EVA	ss5403321712	Oct 13, 2022 (156)
78	HUGCELL_USP	ss5484406846	Oct 13, 2022 (156)
79	1000G_HIGH_COVERAGE	ss5586247825	Oct 13, 2022 (156)
80	EVA	ss5623955877	Oct 13, 2022 (156)
81	EVA	ss5624027479	Oct 13, 2022 (156)
82	SANFORD_IMAGENETICS	ss5652399005	Oct 13, 2022 (156)
83	TOMMO_GENOMICS	ss5753290237	Oct 13, 2022 (156)
84	EVA	ss5800173323	Oct 13, 2022 (156)
85	YY_MCH	ss5812919427	Oct 13, 2022 (156)
86	EVA	ss5837454679	Oct 13, 2022 (156)
87	EVA	ss5848341736	Oct 13, 2022 (156)
88	EVA	ss5850220524	Oct 13, 2022 (156)
89	EVA	ss5922331138	Oct 13, 2022 (156)
90	EVA	ss5936551220	Oct 13, 2022 (156)
91	EVA	ss5943747510	Oct 13, 2022 (156)
92	EVA	ss5980712964	Oct 13, 2022 (156)
93	EVA	ss5981272434	Oct 13, 2022 (156)
94	1000Genomes	NC_000011.9 - 133792021	Oct 12, 2018 (152)
95	1000Genomes_30x	NC_000011.10 - 133922126	Oct 13, 2022 (156)
96	The Avon Longitudinal Study of Parents and Children	NC_000011.9 - 133792021	Oct 12, 2018 (152)
97	Genetic variation in the Estonian population	NC_000011.9 - 133792021	Oct 12, 2018 (152)
98	The Danish reference pan genome	NC_000011.9 - 133792021	Apr 26, 2020 (154)
99	gnomAD - Genomes	NC_000011.10 - 133922126	Apr 26, 2021 (155)
100	GO Exome Sequencing Project	NC_000011.9 - 133792021	Oct 12, 2018 (152)
101	Genome of the Netherlands Release 5	NC_000011.9 - 133792021	Apr 26, 2020 (154)
102	KOREAN population from KRGDB	NC_000011.9 - 133792021	Apr 26, 2020 (154)
103	Korean Genome Project	NC_000011.10 - 133922126	Apr 26, 2020 (154)
104	Medical Genome Project healthy controls from Spanish population	NC_000011.9 - 133792021	Apr 26, 2020 (154)
105	Northern Sweden	NC_000011.9 - 133792021	Jul 13, 2019 (153)
106	Qatari	NC_000011.9 - 133792021	Apr 26, 2020 (154)
107	SGDP_PRJ	NC_000011.9 - 133792021	Apr 26, 2020 (154)
108	Siberian	NC_000011.9 - 133792021	Apr 26, 2020 (154)
109	8.3KJPN	NC_000011.9 - 133792021	Apr 26, 2021 (155)
110	14KJPN	NC_000011.10 - 133922126	Oct 13, 2022 (156)
111	TopMed	NC_000011.10 - 133922126	Apr 26, 2021 (155)
112	UK 10K study - Twins	NC_000011.9 - 133792021	Oct 12, 2018 (152)
113	A Vietnamese Genetic Variation Database	NC_000011.9 - 133792021	Jul 13, 2019 (153)
114	ALFA	NC_000011.10 - 133922126	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)
rs4937859	Sep 24, 2004 (123)
rs60011714	May 25, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss77307522, ss84968440, ss88896218, ss111330673, ss115408046, ss119989420, ss168816864, ss171232656, ss175322567, ss203422465, ss207925605, ss255417874, ss281234745, ss286487004, ss291174296, ss1598809475	NC_000011.8:133297230:T:C	NC_000011.10:133922125:T:C	(self)
56235666, 31229666, 22118310, 2803544, 1147503, 13931193, 33145813, 430794, 11969989, 14538019, 29498467, 7829403, 62597114, 31229666, 6928202, ss225554939, ss235785335, ss242371710, ss535425493, ss562933309, ss658456711, ss713060596, ss989138391, ss1078176673, ss1343630430, ss1426812296, ss1576055521, ss1627825657, ss1670819690, ss1711315034, ss1807074462, ss1932496089, ss2026995841, ss2155313049, ss2627974324, ss2699629322, ss2906294115, ss3009045542, ss3349872720, ss3626791550, ss3646435141, ss3676380062, ss3738685124, ss3750021925, ss3787112677, ss3792230399, ss3797113008, ss3824689992, ss3825813551, ss3832923384, ss3840024760, ss3877481487, ss3925968419, ss3984017731, ss3986552746, ss5204627807, ss5403321712, ss5623955877, ss5624027479, ss5652399005, ss5800173323, ss5837454679, ss5848341736, ss5936551220, ss5943747510, ss5980712964, ss5981272434	NC_000011.9:133792020:T:C	NC_000011.10:133922125:T:C	(self)
73773760, 396651026, 27465920, 87127341, 121172214, 1142152945, ss2187070350, ss3027300402, ss3649741137, ss3692924948, ss3815342212, ss3845507510, ss3971087919, ss4905626558, ss5237217618, ss5289475136, ss5484406846, ss5586247825, ss5753290237, ss5812919427, ss5850220524, ss5922331138	NC_000011.10:133922125:T:C	NC_000011.10:133922125:T:C	(self)
ss16144243, ss19194625, ss20799857	NT_033899.6:37335807:T:C	NC_000011.10:133922125:T:C	(self)
ss768302, ss6829457, ss97429046, ss106780551, ss132941820, ss156983295	NT_033899.8:37354436:T:C	NC_000011.10:133922125:T:C	(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 rs596430

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

rs596430