Name: rs3848551
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.

rs3848551

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr19:49896722 (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>G / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.059549 (15762/264690, TOPMED)
T=0.07831 (2213/28258, 14KJPN)
T=0.00358 (65/18178, ALFA) (+ 12 more)
T=0.07852 (1316/16760, 8.3KJPN)
T=0.0764 (489/6404, 1000G_30x)
T=0.0741 (371/5008, 1000G)
T=0.0007 (3/4480, Estonian)
T=0.0021 (8/3854, ALSPAC)
T=0.0008 (3/3708, TWINSUK)
T=0.1198 (351/2930, KOREAN)
T=0.009 (2/216, Qatari)
T=0.096 (20/208, Vietnamese)
C=0.45 (33/74, SGDP_PRJ)
C=0.5 (1/2, Siberian)
T=0.5 (1/2, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: IL4I1 : 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	18178	C=0.99642	G=0.00000, T=0.00358
European	Sub	14258	C=0.99930	G=0.00000, T=0.00070
African	Sub	2488	C=0.9799	G=0.0000, T=0.0201
African Others	Sub	86	C=0.97	G=0.00, T=0.03
African American	Sub	2402	C=0.9804	G=0.0000, T=0.0196
Asian	Sub	84	C=0.99	G=0.00, T=0.01
East Asian	Sub	68	C=0.99	G=0.00, T=0.01
Other Asian	Sub	16	C=1.00	G=0.00, T=0.00
Latin American 1	Sub	134	C=1.000	G=0.000, T=0.000
Latin American 2	Sub	466	C=1.000	G=0.000, T=0.000
South Asian	Sub	94	C=1.00	G=0.00, T=0.00
Other	Sub	654	C=0.994	G=0.000, T=0.006

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=0.940451	T=0.059549
14KJPN	JAPANESE	Study-wide	28258	C=0.92169	T=0.07831
Allele Frequency Aggregator	Total	Global	18178	C=0.99642	G=0.00000, T=0.00358
Allele Frequency Aggregator	European	Sub	14258	C=0.99930	G=0.00000, T=0.00070
Allele Frequency Aggregator	African	Sub	2488	C=0.9799	G=0.0000, T=0.0201
Allele Frequency Aggregator	Other	Sub	654	C=0.994	G=0.000, T=0.006
Allele Frequency Aggregator	Latin American 2	Sub	466	C=1.000	G=0.000, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	134	C=1.000	G=0.000, T=0.000
Allele Frequency Aggregator	South Asian	Sub	94	C=1.00	G=0.00, T=0.00
Allele Frequency Aggregator	Asian	Sub	84	C=0.99	G=0.00, T=0.01
8.3KJPN	JAPANESE	Study-wide	16760	C=0.92148	T=0.07852
1000Genomes_30x	Global	Study-wide	6404	C=0.9236	T=0.0764
1000Genomes_30x	African	Sub	1786	C=0.8914	T=0.1086
1000Genomes_30x	Europe	Sub	1266	C=0.9961	T=0.0039
1000Genomes_30x	South Asian	Sub	1202	C=0.9834	T=0.0166
1000Genomes_30x	East Asian	Sub	1170	C=0.8846	T=0.1154
1000Genomes_30x	American	Sub	980	C=0.862	T=0.138
1000Genomes	Global	Study-wide	5008	C=0.9259	T=0.0741
1000Genomes	African	Sub	1322	C=0.8896	T=0.1104
1000Genomes	East Asian	Sub	1008	C=0.8859	T=0.1141
1000Genomes	Europe	Sub	1006	C=0.9970	T=0.0030
1000Genomes	South Asian	Sub	978	C=0.983	T=0.017
1000Genomes	American	Sub	694	C=0.870	T=0.130
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.9993	T=0.0007
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.9979	T=0.0021
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.9992	T=0.0008
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.8802	T=0.1198
Qatari	Global	Study-wide	216	C=0.991	T=0.009
A Vietnamese Genetic Variation Database	Global	Study-wide	208	C=0.904	T=0.096
SGDP_PRJ	Global	Study-wide	74	C=0.45	T=0.55
Siberian	Global	Study-wide	2	C=0.5	T=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 19	NC_000019.10:g.49896722C>G
GRCh38.p14 chr 19	NC_000019.10:g.49896722C>T
GRCh37.p13 chr 19	NC_000019.9:g.50399979C>G
GRCh37.p13 chr 19	NC_000019.9:g.50399979C>T
IL4I1 RefSeqGene	NG_021170.1:g.37784G>C
IL4I1 RefSeqGene	NG_021170.1:g.37784G>A

Gene: IL4I1, interleukin 4 induced 1 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
IL4I1 transcript variant 3	NM_001258017.2:c.80-669G>C	N/A	Intron Variant
IL4I1 transcript variant 4	NM_001258018.2:c.80-669G>C	N/A	Intron Variant
IL4I1 transcript variant 6	NM_001385639.1:c.-23+113G… NM_001385639.1:c.-23+113G>C	N/A	Intron Variant
IL4I1 transcript variant 1	NM_152899.2:c.-23+113G>C	N/A	Intron Variant
IL4I1 transcript variant 2	NM_172374.3:c.80-669G>C	N/A	Intron Variant
IL4I1 transcript variant 5	NR_047577.2:n.	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=	G	T
GRCh38.p14 chr 19	NC_000019.10:g.49896722=	NC_000019.10:g.49896722C>G	NC_000019.10:g.49896722C>T
GRCh37.p13 chr 19	NC_000019.9:g.50399979=	NC_000019.9:g.50399979C>G	NC_000019.9:g.50399979C>T
IL4I1 RefSeqGene	NG_021170.1:g.37784=	NG_021170.1:g.37784G>C	NG_021170.1:g.37784G>A
IL4I1 transcript variant 3	NM_001258017.1:c.80-669=	NM_001258017.1:c.80-669G>C	NM_001258017.1:c.80-669G>A
IL4I1 transcript variant 3	NM_001258017.2:c.80-669=	NM_001258017.2:c.80-669G>C	NM_001258017.2:c.80-669G>A
IL4I1 transcript variant 4	NM_001258018.1:c.80-669=	NM_001258018.1:c.80-669G>C	NM_001258018.1:c.80-669G>A
IL4I1 transcript variant 4	NM_001258018.2:c.80-669=	NM_001258018.2:c.80-669G>C	NM_001258018.2:c.80-669G>A
IL4I1 transcript variant 6	NM_001385639.1:c.-23+113=	NM_001385639.1:c.-23+113G>C	NM_001385639.1:c.-23+113G>A
IL4I1 transcript variant 1	NM_152899.1:c.-23+113=	NM_152899.1:c.-23+113G>C	NM_152899.1:c.-23+113G>A
IL4I1 transcript variant 1	NM_152899.2:c.-23+113=	NM_152899.2:c.-23+113G>C	NM_152899.2:c.-23+113G>A
IL4I1 transcript variant 2	NM_172374.2:c.80-669=	NM_172374.2:c.80-669G>C	NM_172374.2:c.80-669G>A
IL4I1 transcript variant 2	NM_172374.3:c.80-669=	NM_172374.3:c.80-669G>C	NM_172374.3:c.80-669G>A
IL4I1 transcript variant X1	XM_005258718.1:c.80-669=	XM_005258718.1:c.80-669G>C	XM_005258718.1:c.80-669G>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#.

46 SubSNP, 16 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss104369	Oct 08, 2002 (108)
2	TSC-CSHL	ss5236551	Oct 08, 2002 (108)
3	TSC-CSHL	ss5342555	Oct 08, 2002 (108)
4	SC_JCM	ss6187681	Feb 20, 2003 (111)
5	WI_SSAHASNP	ss6628842	Feb 20, 2003 (111)
6	CSHL-HAPMAP	ss20072206	Feb 27, 2004 (120)
7	ABI	ss41005161	Mar 13, 2006 (126)
8	HGSV	ss80822948	Dec 14, 2007 (130)
9	ILLUMINA-UK	ss117727305	Dec 01, 2009 (131)
10	COMPLETE_GENOMICS	ss169968450	Jul 04, 2010 (132)
11	BUSHMAN	ss203777519	Jul 04, 2010 (132)
12	GMI	ss283237208	May 04, 2012 (137)
13	1000GENOMES	ss340516925	May 09, 2011 (134)
14	TISHKOFF	ss566031347	Apr 25, 2013 (138)
15	SSMP	ss661898183	Apr 25, 2013 (138)
16	JMKIDD_LAB	ss1081955825	Aug 21, 2014 (142)
17	1000GENOMES	ss1363479387	Aug 21, 2014 (142)
18	EVA_UK10K_ALSPAC	ss1638113722	Apr 01, 2015 (144)
19	EVA_UK10K_TWINSUK	ss1681107755	Apr 01, 2015 (144)
20	EVA_DECODE	ss1698432632	Apr 01, 2015 (144)
21	HAMMER_LAB	ss1809343871	Sep 08, 2015 (146)
22	WEILL_CORNELL_DGM	ss1937877921	Feb 12, 2016 (147)
23	USC_VALOUEV	ss2158262432	Dec 20, 2016 (150)
24	HUMAN_LONGEVITY	ss2226319980	Dec 20, 2016 (150)
25	GRF	ss2702875190	Nov 08, 2017 (151)
26	GNOMAD	ss2963787899	Nov 08, 2017 (151)
27	SWEGEN	ss3017610083	Nov 08, 2017 (151)
28	EGCUT_WGS	ss3684348263	Jul 13, 2019 (153)
29	EVA_DECODE	ss3702926460	Jul 13, 2019 (153)
30	EVA	ss3756155943	Jul 13, 2019 (153)
31	KHV_HUMAN_GENOMES	ss3821405651	Jul 13, 2019 (153)
32	SGDP_PRJ	ss3888391990	Apr 27, 2020 (154)
33	KRGDB	ss3938542534	Apr 27, 2020 (154)
34	TOPMED	ss5077453529	Apr 27, 2021 (155)
35	TOMMO_GENOMICS	ss5228147245	Apr 27, 2021 (155)
36	1000G_HIGH_COVERAGE	ss5307543966	Oct 13, 2022 (156)
37	EVA	ss5435335865	Oct 13, 2022 (156)
38	HUGCELL_USP	ss5500016511	Oct 13, 2022 (156)
39	1000G_HIGH_COVERAGE	ss5613396282	Oct 13, 2022 (156)
40	SANFORD_IMAGENETICS	ss5662554464	Oct 13, 2022 (156)
41	TOMMO_GENOMICS	ss5786913281	Oct 13, 2022 (156)
42	YY_MCH	ss5817671213	Oct 13, 2022 (156)
43	EVA	ss5840661794	Oct 13, 2022 (156)
44	EVA	ss5852318599	Oct 13, 2022 (156)
45	EVA	ss5928408742	Oct 13, 2022 (156)
46	EVA	ss5953960589	Oct 13, 2022 (156)
47	1000Genomes	NC_000019.9 - 50399979	Oct 12, 2018 (152)
48	1000Genomes_30x	NC_000019.10 - 49896722	Oct 13, 2022 (156)
49	The Avon Longitudinal Study of Parents and Children	NC_000019.9 - 50399979	Oct 12, 2018 (152)
50	Genetic variation in the Estonian population	NC_000019.9 - 50399979	Oct 12, 2018 (152)
51	gnomAD - Genomes Submission ignored due to conflicting rows: Row 542336608 (NC_000019.10:49896721:C:G 3/140228) Row 542336609 (NC_000019.10:49896721:C:T 6650/140202)	-	Apr 27, 2021 (155)
52	gnomAD - Genomes Submission ignored due to conflicting rows: Row 542336608 (NC_000019.10:49896721:C:G 3/140228) Row 542336609 (NC_000019.10:49896721:C:T 6650/140202)	-	Apr 27, 2021 (155)
53	KOREAN population from KRGDB	NC_000019.9 - 50399979	Apr 27, 2020 (154)
54	Qatari	NC_000019.9 - 50399979	Apr 27, 2020 (154)
55	SGDP_PRJ	NC_000019.9 - 50399979	Apr 27, 2020 (154)
56	Siberian	NC_000019.9 - 50399979	Apr 27, 2020 (154)
57	8.3KJPN	NC_000019.9 - 50399979	Apr 27, 2021 (155)
58	14KJPN	NC_000019.10 - 49896722	Oct 13, 2022 (156)
59	TopMed	NC_000019.10 - 49896722	Apr 27, 2021 (155)
60	UK 10K study - Twins	NC_000019.9 - 50399979	Oct 12, 2018 (152)
61	A Vietnamese Genetic Variation Database	NC_000019.9 - 50399979	Jul 13, 2019 (153)
62	ALFA	NC_000019.10 - 49896722	Apr 27, 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)
rs57581836	May 23, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss2963787899	NC_000019.9:50399978:C:G	NC_000019.10:49896721:C:G	(self)
3865277179	NC_000019.10:49896721:C:G	NC_000019.10:49896721:C:G	(self)
ss80822948, ss117727305, ss169968450, ss203777519, ss283237208, ss1698432632	NC_000019.8:55091790:C:T	NC_000019.10:49896721:C:T	(self)
76897882, 42573213, 30086511, 45719928, 19919843, 40408970, 10778786, 86116552, 42573213, 9398950, ss340516925, ss566031347, ss661898183, ss1081955825, ss1363479387, ss1638113722, ss1681107755, ss1809343871, ss1937877921, ss2158262432, ss2702875190, ss2963787899, ss3017610083, ss3684348263, ss3756155943, ss3888391990, ss3938542534, ss5228147245, ss5435335865, ss5662554464, ss5840661794, ss5953960589	NC_000019.9:50399978:C:T	NC_000019.10:49896721:C:T	(self)
100922217, 120750385, 292999193, 3865277179, ss2226319980, ss3702926460, ss3821405651, ss5077453529, ss5307543966, ss5500016511, ss5613396282, ss5786913281, ss5817671213, ss5852318599, ss5928408742	NC_000019.10:49896721:C:T	NC_000019.10:49896721:C:T	(self)
ss20072206	NT_011109.15:22668168:C:T	NC_000019.10:49896721:C:T	(self)
ss104369, ss5236551, ss5342555, ss6187681, ss6628842, ss41005161	NT_011109.16:22668196:C:T	NC_000019.10:49896721: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 rs3848551

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

rs3848551