Name: rs76105852
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.

rs76105852

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr2:32254640 (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 / C>G / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.087200 (23081/264690, TOPMED)
G=0.095620 (11104/116126, GnomAD)
G=0.01922 (228/11862, ALFA) (+ 14 more)
G=0.0892 (571/6404, 1000G_30x)
G=0.0901 (451/5008, 1000G)
G=0.0581 (251/4322, Estonian)
G=0.0880 (339/3854, ALSPAC)
G=0.0895 (332/3708, TWINSUK)
G=0.0940 (275/2924, KOREAN)
G=0.0899 (164/1824, Korea1K)
G=0.081 (81/998, GoNL)
G=0.057 (33/574, NorthernSweden)
G=0.204 (44/216, Qatari)
C=0.45 (37/82, SGDP_PRJ)
G=0.07 (3/40, GENOME_DK)
C=0.5 (1/2, Siberian)
G=0.5 (1/2, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: NLRC4 : 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	11862	C=0.98078	G=0.01922, T=0.00000
European	Sub	8192	C=0.9731	G=0.0269, T=0.0000
African	Sub	2440	C=0.9975	G=0.0025, T=0.0000
African Others	Sub	96	C=1.00	G=0.00, T=0.00
African American	Sub	2344	C=0.9974	G=0.0026, T=0.0000
Asian	Sub	90	C=0.99	G=0.01, T=0.00
East Asian	Sub	70	C=1.00	G=0.00, T=0.00
Other Asian	Sub	20	C=0.95	G=0.05, T=0.00
Latin American 1	Sub	116	C=1.000	G=0.000, T=0.000
Latin American 2	Sub	534	C=1.000	G=0.000, T=0.000
South Asian	Sub	80	C=1.00	G=0.00, T=0.00
Other	Sub	410	C=0.998	G=0.002, T=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	C=0.912800	G=0.087200
gnomAD - Genomes	Global	Study-wide	116126	C=0.904380	G=0.095620
gnomAD - Genomes	European	Sub	65400	C=0.90125	G=0.09875
gnomAD - Genomes	African	Sub	33152	C=0.91705	G=0.08295
gnomAD - Genomes	American	Sub	9842	C=0.9166	G=0.0834
gnomAD - Genomes	Ashkenazi Jewish	Sub	3150	C=0.7781	G=0.2219
gnomAD - Genomes	East Asian	Sub	2868	C=0.9226	G=0.0774
gnomAD - Genomes	Other	Sub	1714	C=0.9102	G=0.0898
Allele Frequency Aggregator	Total	Global	11862	C=0.98078	G=0.01922, T=0.00000
Allele Frequency Aggregator	European	Sub	8192	C=0.9731	G=0.0269, T=0.0000
Allele Frequency Aggregator	African	Sub	2440	C=0.9975	G=0.0025, T=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	534	C=1.000	G=0.000, T=0.000
Allele Frequency Aggregator	Other	Sub	410	C=0.998	G=0.002, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	116	C=1.000	G=0.000, T=0.000
Allele Frequency Aggregator	Asian	Sub	90	C=0.99	G=0.01, T=0.00
Allele Frequency Aggregator	South Asian	Sub	80	C=1.00	G=0.00, T=0.00
1000Genomes_30x	Global	Study-wide	6404	C=0.9108	G=0.0892
1000Genomes_30x	African	Sub	1786	C=0.9272	G=0.0728
1000Genomes_30x	Europe	Sub	1266	C=0.9021	G=0.0979
1000Genomes_30x	South Asian	Sub	1202	C=0.9027	G=0.0973
1000Genomes_30x	East Asian	Sub	1170	C=0.8786	G=0.1214
1000Genomes_30x	American	Sub	980	C=0.941	G=0.059
1000Genomes	Global	Study-wide	5008	C=0.9099	G=0.0901
1000Genomes	African	Sub	1322	C=0.9327	G=0.0673
1000Genomes	East Asian	Sub	1008	C=0.8790	G=0.1210
1000Genomes	Europe	Sub	1006	C=0.9046	G=0.0954
1000Genomes	South Asian	Sub	978	C=0.897	G=0.103
1000Genomes	American	Sub	694	C=0.938	G=0.062
Genetic variation in the Estonian population	Estonian	Study-wide	4322	C=0.9419	G=0.0581
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.9120	G=0.0880
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.9105	G=0.0895
KOREAN population from KRGDB	KOREAN	Study-wide	2924	C=0.9060	G=0.0940
Korean Genome Project	KOREAN	Study-wide	1824	C=0.9101	G=0.0899
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.919	G=0.081
Northern Sweden	ACPOP	Study-wide	574	C=0.943	G=0.057
Qatari	Global	Study-wide	216	C=0.796	G=0.204
SGDP_PRJ	Global	Study-wide	82	C=0.45	G=0.55
The Danish reference pan genome	Danish	Study-wide	40	C=0.93	G=0.07
Siberian	Global	Study-wide	2	C=0.5	G=0.5

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 2	NC_000002.12:g.32254640C>A
GRCh38.p14 chr 2	NC_000002.12:g.32254640C>G
GRCh38.p14 chr 2	NC_000002.12:g.32254640C>T
GRCh37.p13 chr 2	NC_000002.11:g.32479709C>A
GRCh37.p13 chr 2	NC_000002.11:g.32479709C>G
GRCh37.p13 chr 2	NC_000002.11:g.32479709C>T
Incomplete genomic	NG_041780.1:g.16104G>T
Incomplete genomic	NG_041780.1:g.16104G>C
Incomplete genomic	NG_041780.1:g.16104G>A

Gene: NLRC4, NLR family CARD domain containing 4 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
Protein-coding transcripts	NM_001199138.2:c.2-1961G>T	N/A	Intron Variant
Protein-coding transcripts	NM_001199139.1:c.2-1961G>T	N/A	Intron Variant
Protein-coding transcripts	NM_001302504.1:c.2-1961G>T	N/A	Intron Variant
Protein-coding transcripts	NM_021209.4:c.2-1961G>T	N/A	Intron Variant
Predicted protein-coding transcript	XM_047445356.1:c.2-1961G>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	G	T
GRCh38.p14 chr 2	NC_000002.12:g.32254640=	NC_000002.12:g.32254640C>A	NC_000002.12:g.32254640C>G	NC_000002.12:g.32254640C>T
GRCh37.p13 chr 2	NC_000002.11:g.32479709=	NC_000002.11:g.32479709C>A	NC_000002.11:g.32479709C>G	NC_000002.11:g.32479709C>T
Incomplete genomic	NG_041780.1:g.16104=	NG_041780.1:g.16104G>T	NG_041780.1:g.16104G>C	NG_041780.1:g.16104G>A
Protein-coding transcripts	NM_001199138.1:c.2-1961=	NM_001199138.1:c.2-1961G>T	NM_001199138.1:c.2-1961G>C	NM_001199138.1:c.2-1961G>A
Protein-coding transcripts	NM_001199138.2:c.2-1961=	NM_001199138.2:c.2-1961G>T	NM_001199138.2:c.2-1961G>C	NM_001199138.2:c.2-1961G>A
Protein-coding transcripts	NM_001199139.1:c.2-1961=	NM_001199139.1:c.2-1961G>T	NM_001199139.1:c.2-1961G>C	NM_001199139.1:c.2-1961G>A
Protein-coding transcripts	NM_001302504.1:c.2-1961=	NM_001302504.1:c.2-1961G>T	NM_001302504.1:c.2-1961G>C	NM_001302504.1:c.2-1961G>A
Protein-coding transcripts	NM_021209.4:c.2-1961=	NM_021209.4:c.2-1961G>T	NM_021209.4:c.2-1961G>C	NM_021209.4:c.2-1961G>A
Predicted protein-coding transcript	XM_047445356.1:c.2-1961=	XM_047445356.1:c.2-1961G>T	XM_047445356.1:c.2-1961G>C	XM_047445356.1:c.2-1961G>A

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#.

44 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	BGI	ss103470538	Dec 01, 2009 (131)
2	COMPLETE_GENOMICS	ss166371840	Jul 04, 2010 (132)
3	1000GENOMES	ss219153115	Jul 14, 2010 (132)
4	1000GENOMES	ss231099601	Jul 14, 2010 (132)
5	TISHKOFF	ss555454427	Apr 25, 2013 (138)
6	EVA-GONL	ss976650669	Aug 21, 2014 (142)
7	1000GENOMES	ss1296537333	Aug 21, 2014 (142)
8	DDI	ss1428524980	Apr 01, 2015 (144)
9	EVA_GENOME_DK	ss1578805495	Apr 01, 2015 (144)
10	EVA_DECODE	ss1586057810	Apr 01, 2015 (144)
11	EVA_UK10K_ALSPAC	ss1603144275	Apr 01, 2015 (144)
12	EVA_UK10K_TWINSUK	ss1646138308	Apr 01, 2015 (144)
13	WEILL_CORNELL_DGM	ss1919883113	Feb 12, 2016 (147)
14	USC_VALOUEV	ss2148515289	Dec 20, 2016 (150)
15	HUMAN_LONGEVITY	ss2228824689	Dec 20, 2016 (150)
16	GRF	ss2703076702	Nov 08, 2017 (151)
17	GNOMAD	ss2771498973	Nov 08, 2017 (151)
18	SWEGEN	ss2989228427	Nov 08, 2017 (151)
19	BIOINF_KMB_FNS_UNIBA	ss3024001778	Nov 08, 2017 (151)
20	CSHL	ss3344146401	Nov 08, 2017 (151)
21	EGCUT_WGS	ss3657185792	Jul 13, 2019 (153)
22	EVA_DECODE	ss3703557284	Jul 13, 2019 (153)
23	ACPOP	ss3728286862	Jul 13, 2019 (153)
24	EVA	ss3756547624	Jul 13, 2019 (153)
25	KHV_HUMAN_GENOMES	ss3800925414	Jul 13, 2019 (153)
26	EVA	ss3826897655	Apr 25, 2020 (154)
27	SGDP_PRJ	ss3851913763	Apr 25, 2020 (154)
28	KRGDB	ss3897336839	Apr 25, 2020 (154)
29	KOGIC	ss3947424719	Apr 25, 2020 (154)
30	TOPMED	ss4499599510	Apr 26, 2021 (155)
31	TOMMO_GENOMICS	ss5150576435	Apr 26, 2021 (155)
32	TOMMO_GENOMICS	ss5150576436	Apr 26, 2021 (155)
33	1000G_HIGH_COVERAGE	ss5247460323	Oct 17, 2022 (156)
34	EVA	ss5327821062	Oct 17, 2022 (156)
35	HUGCELL_USP	ss5447718984	Oct 17, 2022 (156)
36	EVA	ss5506344850	Oct 17, 2022 (156)
37	1000G_HIGH_COVERAGE	ss5522360250	Oct 17, 2022 (156)
38	SANFORD_IMAGENETICS	ss5628401302	Oct 17, 2022 (156)
39	TOMMO_GENOMICS	ss5678974113	Oct 17, 2022 (156)
40	TOMMO_GENOMICS	ss5678974114	Oct 17, 2022 (156)
41	YY_MCH	ss5802057017	Oct 17, 2022 (156)
42	EVA	ss5819865721	Oct 17, 2022 (156)
43	EVA	ss5929662412	Oct 17, 2022 (156)
44	EVA	ss5954608565	Oct 17, 2022 (156)
45	1000Genomes	NC_000002.11 - 32479709	Oct 11, 2018 (152)
46	1000Genomes_30x	NC_000002.12 - 32254640	Oct 17, 2022 (156)
47	The Avon Longitudinal Study of Parents and Children	NC_000002.11 - 32479709	Oct 11, 2018 (152)
48	Genetic variation in the Estonian population	NC_000002.11 - 32479709	Oct 11, 2018 (152)
49	The Danish reference pan genome	NC_000002.11 - 32479709	Apr 25, 2020 (154)
50	gnomAD - Genomes	NC_000002.12 - 32254640	Apr 26, 2021 (155)
51	Genome of the Netherlands Release 5	NC_000002.11 - 32479709	Apr 25, 2020 (154)
52	KOREAN population from KRGDB	NC_000002.11 - 32479709	Apr 25, 2020 (154)
53	Korean Genome Project	NC_000002.12 - 32254640	Apr 25, 2020 (154)
54	Northern Sweden	NC_000002.11 - 32479709	Jul 13, 2019 (153)
55	Qatari	NC_000002.11 - 32479709	Apr 25, 2020 (154)
56	SGDP_PRJ	NC_000002.11 - 32479709	Apr 25, 2020 (154)
57	Siberian	NC_000002.11 - 32479709	Apr 25, 2020 (154)
58	8.3KJPN Submission ignored due to conflicting rows: Row 8545742 (NC_000002.11:32479708:C:G 1796/16748) Row 8545743 (NC_000002.11:32479708:C:A 26/16748)	-	Apr 26, 2021 (155)
59	8.3KJPN Submission ignored due to conflicting rows: Row 8545742 (NC_000002.11:32479708:C:G 1796/16748) Row 8545743 (NC_000002.11:32479708:C:A 26/16748)	-	Apr 26, 2021 (155)
60	14KJPN Submission ignored due to conflicting rows: Row 12811217 (NC_000002.12:32254639:C:G 2847/28122) Row 12811218 (NC_000002.12:32254639:C:A 32/28122)	-	Oct 17, 2022 (156)
61	14KJPN Submission ignored due to conflicting rows: Row 12811217 (NC_000002.12:32254639:C:G 2847/28122) Row 12811218 (NC_000002.12:32254639:C:A 32/28122)	-	Oct 17, 2022 (156)
62	TopMed	NC_000002.12 - 32254640	Apr 26, 2021 (155)
63	UK 10K study - Twins	NC_000002.11 - 32479709	Oct 11, 2018 (152)
64	ALFA	NC_000002.12 - 32254640	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
ss5150576436	NC_000002.11:32479708:C:A	NC_000002.12:32254639:C:A	(self)
ss5678974114	NC_000002.12:32254639:C:A	NC_000002.12:32254639:C:A
ss166371840, ss1586057810	NC_000002.10:32333212:C:G	NC_000002.12:32254639:C:G	(self)
7460271, 4143323, 2924040, 4980886, 1819163, 4514233, 1571727, 1925043, 3930743, 1031643, 4143323, ss219153115, ss231099601, ss555454427, ss976650669, ss1296537333, ss1428524980, ss1578805495, ss1603144275, ss1646138308, ss1919883113, ss2148515289, ss2703076702, ss2771498973, ss2989228427, ss3344146401, ss3657185792, ss3728286862, ss3756547624, ss3826897655, ss3851913763, ss3897336839, ss5150576435, ss5327821062, ss5506344850, ss5628401302, ss5819865721, ss5954608565	NC_000002.11:32479708:C:G	NC_000002.12:32254639:C:G	(self)
9886185, 52993199, 3802720, 303422389, 12745906311, ss2228824689, ss3024001778, ss3703557284, ss3800925414, ss3947424719, ss4499599510, ss5247460323, ss5447718984, ss5522360250, ss5678974113, ss5802057017, ss5929662412	NC_000002.12:32254639:C:G	NC_000002.12:32254639:C:G	(self)
ss103470538	NT_022184.15:11301595:C:G	NC_000002.12:32254639:C:G	(self)
12745906311	NC_000002.12:32254639:C:T	NC_000002.12:32254639:C:T	(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 rs76105852

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

rs76105852