Name: rs35000415
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.

rs35000415

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr7:128945562 (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>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.087041 (23039/264690, TOPMED)
T=0.088514 (12407/140170, GnomAD)
T=0.13119 (3568/27198, ALFA) (+ 12 more)
T=0.0600 (384/6404, 1000G_30x)
T=0.0587 (294/5008, 1000G)
T=0.1592 (713/4480, Estonian)
T=0.1160 (447/3854, ALSPAC)
T=0.1146 (425/3708, TWINSUK)
T=0.0007 (2/2922, KOREAN)
T=0.101 (101/998, GoNL)
T=0.152 (91/600, NorthernSweden)
T=0.106 (23/216, Qatari)
C=0.40 (38/96, SGDP_PRJ)
T=0.10 (4/40, GENOME_DK)
C=0.41 (9/22, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: IRF5 : Intron Variant
Publications: 1 citation
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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	Alt HMOZ	HTRZ	HWEP
Total	Global	27198	C=0.86881	T=0.13119	0.760644	0.023016	0.216339	19
European	Sub	15796	C=0.87313	T=0.12687	0.761585	0.01532	0.223094	0
African	Sub	3244	C=0.9809	T=0.0191	0.961776	0.0	0.038224	0
African Others	Sub	114	C=1.000	T=0.000	1.0	0.0	0.0	N/A
African American	Sub	3130	C=0.9802	T=0.0198	0.960383	0.0	0.039617	0
Asian	Sub	134	C=1.000	T=0.000	1.0	0.0	0.0	N/A
East Asian	Sub	104	C=1.000	T=0.000	1.0	0.0	0.0	N/A
Other Asian	Sub	30	C=1.00	T=0.00	1.0	0.0	0.0	N/A
Latin American 1	Sub	222	C=0.910	T=0.090	0.81982	0.0	0.18018	1
Latin American 2	Sub	4680	C=0.7545	T=0.2455	0.582051	0.073077	0.344872	7
South Asian	Sub	112	C=0.777	T=0.223	0.607143	0.053571	0.339286	0
Other	Sub	3010	C=0.8977	T=0.1023	0.807309	0.01196	0.180731	0

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=0.912959	T=0.087041
gnomAD - Genomes	Global	Study-wide	140170	C=0.911486	T=0.088514
gnomAD - Genomes	European	Sub	75902	C=0.88377	T=0.11623
gnomAD - Genomes	African	Sub	42012	C=0.97498	T=0.02502
gnomAD - Genomes	American	Sub	13650	C=0.85788	T=0.14212
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	C=0.8858	T=0.1142
gnomAD - Genomes	East Asian	Sub	3134	C=0.9987	T=0.0013
gnomAD - Genomes	Other	Sub	2152	C=0.9020	T=0.0980
Allele Frequency Aggregator	Total	Global	27198	C=0.86881	T=0.13119
Allele Frequency Aggregator	European	Sub	15796	C=0.87313	T=0.12687
Allele Frequency Aggregator	Latin American 2	Sub	4680	C=0.7545	T=0.2455
Allele Frequency Aggregator	African	Sub	3244	C=0.9809	T=0.0191
Allele Frequency Aggregator	Other	Sub	3010	C=0.8977	T=0.1023
Allele Frequency Aggregator	Latin American 1	Sub	222	C=0.910	T=0.090
Allele Frequency Aggregator	Asian	Sub	134	C=1.000	T=0.000
Allele Frequency Aggregator	South Asian	Sub	112	C=0.777	T=0.223
1000Genomes_30x	Global	Study-wide	6404	C=0.9400	T=0.0600
1000Genomes_30x	African	Sub	1786	C=0.9950	T=0.0050
1000Genomes_30x	Europe	Sub	1266	C=0.8997	T=0.1003
1000Genomes_30x	South Asian	Sub	1202	C=0.8586	T=0.1414
1000Genomes_30x	East Asian	Sub	1170	C=0.9983	T=0.0017
1000Genomes_30x	American	Sub	980	C=0.922	T=0.078
1000Genomes	Global	Study-wide	5008	C=0.9413	T=0.0587
1000Genomes	African	Sub	1322	C=0.9939	T=0.0061
1000Genomes	East Asian	Sub	1008	C=0.9980	T=0.0020
1000Genomes	Europe	Sub	1006	C=0.8996	T=0.1004
1000Genomes	South Asian	Sub	978	C=0.866	T=0.134
1000Genomes	American	Sub	694	C=0.925	T=0.075
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.8408	T=0.1592
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.8840	T=0.1160
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.8854	T=0.1146
KOREAN population from KRGDB	KOREAN	Study-wide	2922	C=0.9993	T=0.0007
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.899	T=0.101
Northern Sweden	ACPOP	Study-wide	600	C=0.848	T=0.152
Qatari	Global	Study-wide	216	C=0.894	T=0.106
SGDP_PRJ	Global	Study-wide	96	C=0.40	T=0.60
The Danish reference pan genome	Danish	Study-wide	40	C=0.90	T=0.10
Siberian	Global	Study-wide	22	C=0.41	T=0.59

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 7	NC_000007.14:g.128945562C>T
GRCh37.p13 chr 7	NC_000007.13:g.128585616C>T
IRF5 RefSeqGene	NG_012306.2:g.13532C>T
IRF5 RefSeqGene	NG_012306.1:g.12623C>T

Gene: IRF5, interferon regulatory factor 5 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
IRF5 transcript variant 3	NM_001098627.4:c.196-283C… NM_001098627.4:c.196-283C>T	N/A	Intron Variant
IRF5 transcript variant 5	NM_001098629.3:c.196-283C… NM_001098629.3:c.196-283C>T	N/A	Intron Variant
IRF5 transcript variant 6	NM_001098630.3:c.196-283C… NM_001098630.3:c.196-283C>T	N/A	Intron Variant
IRF5 transcript variant 8	NM_001242452.3:c.196-283C… NM_001242452.3:c.196-283C>T	N/A	Intron Variant
IRF5 transcript variant 9	NM_001347928.2:c.196-283C… NM_001347928.2:c.196-283C>T	N/A	Intron Variant
IRF5 transcript variant 10	NM_001364314.2:c.196-283C… NM_001364314.2:c.196-283C>T	N/A	Intron Variant
IRF5 transcript variant 2	NM_032643.5:c.196-283C>T	N/A	Intron Variant
IRF5 transcript variant X1	XM_006715974.3:c.196-283C… XM_006715974.3:c.196-283C>T	N/A	Intron Variant
IRF5 transcript variant X4	XM_011516158.4:c.196-283C… XM_011516158.4:c.196-283C>T	N/A	Intron Variant
IRF5 transcript variant X2	XM_011516159.4:c.196-283C… XM_011516159.4:c.196-283C>T	N/A	Intron Variant
IRF5 transcript variant X3	XM_011516160.2:c.196-283C… XM_011516160.2:c.196-283C>T	N/A	Intron Variant
IRF5 transcript variant X5	XM_047420336.1:c.196-283C… XM_047420336.1:c.196-283C>T	N/A	Intron Variant
IRF5 transcript variant X6	XM_047420337.1:c.196-283C… XM_047420337.1:c.196-283C>T	N/A	Intron Variant
IRF5 transcript variant X7	XM_047420338.1:c.196-283C… XM_047420338.1:c.196-283C>T	N/A	Intron Variant
IRF5 transcript variant X8	XM_047420339.1:c.196-283C… XM_047420339.1:c.196-283C>T	N/A	Intron Variant
IRF5 transcript variant X9	XM_047420340.1:c.196-283C… XM_047420340.1:c.196-283C>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=	T
GRCh38.p14 chr 7	NC_000007.14:g.128945562=	NC_000007.14:g.128945562C>T
GRCh37.p13 chr 7	NC_000007.13:g.128585616=	NC_000007.13:g.128585616C>T
IRF5 RefSeqGene	NG_012306.2:g.13532=	NG_012306.2:g.13532C>T
IRF5 RefSeqGene	NG_012306.1:g.12623=	NG_012306.1:g.12623C>T
IRF5 transcript variant 3	NM_001098627.2:c.196-283=	NM_001098627.2:c.196-283C>T
IRF5 transcript variant 3	NM_001098627.4:c.196-283=	NM_001098627.4:c.196-283C>T
IRF5 transcript variant 5	NM_001098629.1:c.196-283=	NM_001098629.1:c.196-283C>T
IRF5 transcript variant 5	NM_001098629.3:c.196-283=	NM_001098629.3:c.196-283C>T
IRF5 transcript variant 6	NM_001098630.1:c.196-283=	NM_001098630.1:c.196-283C>T
IRF5 transcript variant 6	NM_001098630.3:c.196-283=	NM_001098630.3:c.196-283C>T
IRF5 transcript variant 8	NM_001242452.1:c.196-283=	NM_001242452.1:c.196-283C>T
IRF5 transcript variant 8	NM_001242452.3:c.196-283=	NM_001242452.3:c.196-283C>T
IRF5 transcript variant 9	NM_001347928.2:c.196-283=	NM_001347928.2:c.196-283C>T
IRF5 transcript variant 10	NM_001364314.2:c.196-283=	NM_001364314.2:c.196-283C>T
IRF5 transcript variant 2	NM_032643.3:c.196-283=	NM_032643.3:c.196-283C>T
IRF5 transcript variant 2	NM_032643.5:c.196-283=	NM_032643.5:c.196-283C>T
IRF5 transcript variant X1	XM_005250317.1:c.196-283=	XM_005250317.1:c.196-283C>T
IRF5 transcript variant X2	XM_005250318.1:c.196-283=	XM_005250318.1:c.196-283C>T
IRF5 transcript variant X3	XM_005250319.1:c.196-283=	XM_005250319.1:c.196-283C>T
IRF5 transcript variant X4	XM_005250320.1:c.196-283=	XM_005250320.1:c.196-283C>T
IRF5 transcript variant X5	XM_005250321.1:c.-454-283=	XM_005250321.1:c.-454-283C>T
IRF5 transcript variant X1	XM_006715974.3:c.196-283=	XM_006715974.3:c.196-283C>T
IRF5 transcript variant X4	XM_011516158.4:c.196-283=	XM_011516158.4:c.196-283C>T
IRF5 transcript variant X2	XM_011516159.4:c.196-283=	XM_011516159.4:c.196-283C>T
IRF5 transcript variant X3	XM_011516160.2:c.196-283=	XM_011516160.2:c.196-283C>T
IRF5 transcript variant X5	XM_047420336.1:c.196-283=	XM_047420336.1:c.196-283C>T
IRF5 transcript variant X6	XM_047420337.1:c.196-283=	XM_047420337.1:c.196-283C>T
IRF5 transcript variant X7	XM_047420338.1:c.196-283=	XM_047420338.1:c.196-283C>T
IRF5 transcript variant X8	XM_047420339.1:c.196-283=	XM_047420339.1:c.196-283C>T
IRF5 transcript variant X9	XM_047420340.1:c.196-283=	XM_047420340.1:c.196-283C>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#.

52 SubSNP, 15 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	ABI	ss43055114	Mar 14, 2006 (126)
2	BCMHGSC_JDW	ss93764911	Mar 25, 2008 (130)
3	HUMANGENOME_JCVI	ss98335565	Feb 04, 2009 (130)
4	ENSEMBL	ss142924008	Dec 01, 2009 (131)
5	ENSEMBL	ss143033490	Dec 01, 2009 (131)
6	ILLUMINA	ss161096451	Dec 01, 2009 (131)
7	COMPLETE_GENOMICS	ss162710821	Jul 04, 2010 (132)
8	1000GENOMES	ss234165492	Jul 15, 2010 (132)
9	GMI	ss285717746	Apr 25, 2013 (138)
10	PJP	ss293964984	May 09, 2011 (134)
11	ILLUMINA	ss479395930	Sep 08, 2015 (146)
12	SSMP	ss654711013	Apr 25, 2013 (138)
13	EVA-GONL	ss984795349	Aug 21, 2014 (142)
14	JMKIDD_LAB	ss1074979517	Aug 21, 2014 (142)
15	1000GENOMES	ss1327129936	Aug 21, 2014 (142)
16	EVA_GENOME_DK	ss1582400430	Apr 01, 2015 (144)
17	EVA_DECODE	ss1594384011	Apr 01, 2015 (144)
18	EVA_UK10K_ALSPAC	ss1619210656	Apr 01, 2015 (144)
19	EVA_UK10K_TWINSUK	ss1662204689	Apr 01, 2015 (144)
20	WEILL_CORNELL_DGM	ss1928053460	Feb 12, 2016 (147)
21	JJLAB	ss2024714844	Sep 14, 2016 (149)
22	ILLUMINA	ss2094979610	Dec 20, 2016 (150)
23	ILLUMINA	ss2095203058	Dec 20, 2016 (150)
24	USC_VALOUEV	ss2152935733	Dec 20, 2016 (150)
25	HUMAN_LONGEVITY	ss2297840327	Dec 20, 2016 (150)
26	GNOMAD	ss2859092681	Nov 08, 2017 (151)
27	AFFY	ss2985420290	Nov 08, 2017 (151)
28	SWEGEN	ss3002030259	Nov 08, 2017 (151)
29	BIOINF_KMB_FNS_UNIBA	ss3026146328	Nov 08, 2017 (151)
30	CSHL	ss3347842315	Nov 08, 2017 (151)
31	ILLUMINA	ss3636875901	Oct 12, 2018 (152)
32	URBANLAB	ss3648751518	Oct 12, 2018 (152)
33	ILLUMINA	ss3653313974	Oct 12, 2018 (152)
34	EGCUT_WGS	ss3669786527	Jul 13, 2019 (153)
35	EVA_DECODE	ss3720687248	Jul 13, 2019 (153)
36	ACPOP	ss3735069493	Jul 13, 2019 (153)
37	EVA	ss3767158025	Jul 13, 2019 (153)
38	KHV_HUMAN_GENOMES	ss3810328132	Jul 13, 2019 (153)
39	EVA	ss3830818650	Apr 26, 2020 (154)
40	SGDP_PRJ	ss3868394677	Apr 26, 2020 (154)
41	KRGDB	ss3915740870	Apr 26, 2020 (154)
42	TOPMED	ss4763714850	Apr 26, 2021 (155)
43	1000G_HIGH_COVERAGE	ss5274732568	Oct 14, 2022 (156)
44	EVA	ss5376772113	Oct 14, 2022 (156)
45	HUGCELL_USP	ss5471618925	Oct 14, 2022 (156)
46	EVA	ss5509138319	Oct 14, 2022 (156)
47	1000G_HIGH_COVERAGE	ss5563890042	Oct 14, 2022 (156)
48	SANFORD_IMAGENETICS	ss5643985341	Oct 14, 2022 (156)
49	YY_MCH	ss5809091609	Oct 14, 2022 (156)
50	EVA	ss5823523241	Oct 14, 2022 (156)
51	EVA	ss5860877523	Oct 14, 2022 (156)
52	EVA	ss5973182585	Oct 14, 2022 (156)
53	1000Genomes	NC_000007.13 - 128585616	Oct 12, 2018 (152)
54	1000Genomes_30x	NC_000007.14 - 128945562	Oct 14, 2022 (156)
55	The Avon Longitudinal Study of Parents and Children	NC_000007.13 - 128585616	Oct 12, 2018 (152)
56	Genetic variation in the Estonian population	NC_000007.13 - 128585616	Oct 12, 2018 (152)
57	The Danish reference pan genome	NC_000007.13 - 128585616	Apr 26, 2020 (154)
58	gnomAD - Genomes	NC_000007.14 - 128945562	Apr 26, 2021 (155)
59	Genome of the Netherlands Release 5	NC_000007.13 - 128585616	Apr 26, 2020 (154)
60	KOREAN population from KRGDB	NC_000007.13 - 128585616	Apr 26, 2020 (154)
61	Northern Sweden	NC_000007.13 - 128585616	Jul 13, 2019 (153)
62	Qatari	NC_000007.13 - 128585616	Apr 26, 2020 (154)
63	SGDP_PRJ	NC_000007.13 - 128585616	Apr 26, 2020 (154)
64	Siberian	NC_000007.13 - 128585616	Apr 26, 2020 (154)
65	TopMed	NC_000007.14 - 128945562	Apr 26, 2021 (155)
66	UK 10K study - Twins	NC_000007.13 - 128585616	Oct 12, 2018 (152)
67	ALFA	NC_000007.14 - 128945562	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)
rs62478575	May 23, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss93764911, ss162710821, ss285717746, ss293964984, ss1594384011, ss2094979610	NC_000007.12:128372851:C:T	NC_000007.14:128945561:C:T	(self)
39173418, 21794696, 15524775, 8565368, 9726074, 22918264, 8354358, 10095390, 20411657, 5452087, 21794696, ss234165492, ss479395930, ss654711013, ss984795349, ss1074979517, ss1327129936, ss1582400430, ss1619210656, ss1662204689, ss1928053460, ss2024714844, ss2095203058, ss2152935733, ss2859092681, ss2985420290, ss3002030259, ss3347842315, ss3636875901, ss3653313974, ss3669786527, ss3735069493, ss3767158025, ss3830818650, ss3868394677, ss3915740870, ss5376772113, ss5509138319, ss5643985341, ss5823523241, ss5973182585	NC_000007.13:128585615:C:T	NC_000007.14:128945561:C:T	(self)
51415977, 276609879, 601092409, 9373679748, ss2297840327, ss3026146328, ss3648751518, ss3720687248, ss3810328132, ss4763714850, ss5274732568, ss5471618925, ss5563890042, ss5809091609, ss5860877523	NC_000007.14:128945561:C:T	NC_000007.14:128945561:C:T	(self)
ss43055114, ss98335565, ss142924008, ss143033490, ss161096451	NT_007933.15:66618458:C:T	NC_000007.14:128945561:C:T	(self)

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

1 citation for rs35000415

PMID	Title	Author	Year	Journal
31156624	Circulating Levels of Interferon Regulatory Factor-5 Associates With Subgroups of Systemic Lupus Erythematosus Patients.	Idborg H et al.	2019	Frontiers in immunology

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

rs35000415