Name: rs28416813
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.

rs28416813

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr19:39245004 (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
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.404670 (107112/264690, TOPMED)
G=0.312673 (77750/248662, GnomAD_exome)
G=0.394802 (54943/139166, GnomAD) (+ 14 more)
G=0.317023 (38259/120682, ExAC)
G=0.10404 (2940/28258, 14KJPN)
G=0.36022 (9909/27508, ALFA)
G=0.10519 (1763/16760, 8.3KJPN)
G=0.37519 (4879/13004, GO-ESP)
G=0.3696 (2367/6404, 1000G_30x)
G=0.3528 (1767/5008, 1000G)
G=0.0584 (171/2930, KOREAN)
G=0.318 (317/998, GoNL)
G=0.056 (44/788, PRJEB37584)
G=0.253 (152/600, NorthernSweden)
G=0.195 (104/534, MGP)
C=0.366 (98/268, SGDP_PRJ)
G=0.287 (62/216, Qatari)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: IFNL3 : Intron Variant
Publications: 16 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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	Alt HMOZ	HTRZ	HWEP
Total	Global	27508	C=0.63978	G=0.36022	0.416533	0.136978	0.446488	8
European	Sub	20214	C=0.67171	G=0.32829	0.450678	0.107252	0.44207	0
African	Sub	3492	C=0.4336	G=0.5664	0.190722	0.323597	0.485682	0
African Others	Sub	122	C=0.328	G=0.672	0.163934	0.508197	0.327869	3
African American	Sub	3370	C=0.4374	G=0.5626	0.191691	0.316914	0.491395	0
Asian	Sub	168	C=0.935	G=0.065	0.869048	0.0	0.130952	0
East Asian	Sub	112	C=0.929	G=0.071	0.857143	0.0	0.142857	0
Other Asian	Sub	56	C=0.95	G=0.05	0.892857	0.0	0.107143	0
Latin American 1	Sub	146	C=0.671	G=0.329	0.452055	0.109589	0.438356	0
Latin American 2	Sub	610	C=0.631	G=0.369	0.409836	0.147541	0.442623	0
South Asian	Sub	98	C=0.69	G=0.31	0.428571	0.040816	0.530612	2
Other	Sub	2780	C=0.6471	G=0.3529	0.423741	0.129496	0.446763	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=0.595330	G=0.404670
gnomAD - Exomes	Global	Study-wide	248662	C=0.687327	G=0.312673
gnomAD - Exomes	European	Sub	133978	C=0.697734	G=0.302266
gnomAD - Exomes	Asian	Sub	48808	C=0.83804	G=0.16196
gnomAD - Exomes	American	Sub	34236	C=0.58628	G=0.41372
gnomAD - Exomes	African	Sub	15600	C=0.39019	G=0.60981
gnomAD - Exomes	Ashkenazi Jewish	Sub	9970	C=0.6299	G=0.3701
gnomAD - Exomes	Other	Sub	6070	C=0.6736	G=0.3264
gnomAD - Genomes	Global	Study-wide	139166	C=0.605198	G=0.394802
gnomAD - Genomes	European	Sub	75732	C=0.69759	G=0.30241
gnomAD - Genomes	African	Sub	41264	C=0.39911	G=0.60089
gnomAD - Genomes	American	Sub	13588	C=0.63070	G=0.36930
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	C=0.6202	G=0.3798
gnomAD - Genomes	East Asian	Sub	3126	C=0.9344	G=0.0656
gnomAD - Genomes	Other	Sub	2136	C=0.6433	G=0.3567
ExAC	Global	Study-wide	120682	C=0.682977	G=0.317023
ExAC	Europe	Sub	73050	C=0.68862	G=0.31138
ExAC	Asian	Sub	25142	C=0.83044	G=0.16956
ExAC	American	Sub	11426	C=0.57798	G=0.42202
ExAC	African	Sub	10158	C=0.39398	G=0.60602
ExAC	Other	Sub	906	C=0.700	G=0.300
14KJPN	JAPANESE	Study-wide	28258	C=0.89596	G=0.10404
Allele Frequency Aggregator	Total	Global	27508	C=0.63978	G=0.36022
Allele Frequency Aggregator	European	Sub	20214	C=0.67171	G=0.32829
Allele Frequency Aggregator	African	Sub	3492	C=0.4336	G=0.5664
Allele Frequency Aggregator	Other	Sub	2780	C=0.6471	G=0.3529
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.631	G=0.369
Allele Frequency Aggregator	Asian	Sub	168	C=0.935	G=0.065
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.671	G=0.329
Allele Frequency Aggregator	South Asian	Sub	98	C=0.69	G=0.31
8.3KJPN	JAPANESE	Study-wide	16760	C=0.89481	G=0.10519
GO Exome Sequencing Project	Global	Study-wide	13004	C=0.62481	G=0.37519
GO Exome Sequencing Project	European American	Sub	8598	C=0.7190	G=0.2810
GO Exome Sequencing Project	African American	Sub	4406	C=0.4410	G=0.5590
1000Genomes_30x	Global	Study-wide	6404	C=0.6304	G=0.3696
1000Genomes_30x	African	Sub	1786	C=0.3214	G=0.6786
1000Genomes_30x	Europe	Sub	1266	C=0.6943	G=0.3057
1000Genomes_30x	South Asian	Sub	1202	C=0.7712	G=0.2288
1000Genomes_30x	East Asian	Sub	1170	C=0.9239	G=0.0761
1000Genomes_30x	American	Sub	980	C=0.588	G=0.412
1000Genomes	Global	Study-wide	5008	C=0.6472	G=0.3528
1000Genomes	African	Sub	1322	C=0.3366	G=0.6634
1000Genomes	East Asian	Sub	1008	C=0.9177	G=0.0823
1000Genomes	Europe	Sub	1006	C=0.6889	G=0.3111
1000Genomes	South Asian	Sub	978	C=0.778	G=0.222
1000Genomes	American	Sub	694	C=0.601	G=0.399
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.9416	G=0.0584
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.682	G=0.318
CNV burdens in cranial meningiomas	Global	Study-wide	788	C=0.944	G=0.056
CNV burdens in cranial meningiomas	CRM	Sub	788	C=0.944	G=0.056
Northern Sweden	ACPOP	Study-wide	600	C=0.747	G=0.253
Medical Genome Project healthy controls from Spanish population	Spanish controls	Study-wide	534	C=0.805	G=0.195
SGDP_PRJ	Global	Study-wide	268	C=0.366	G=0.634
Qatari	Global	Study-wide	216	C=0.713	G=0.287

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.39245004C>G
GRCh37.p13 chr 19	NC_000019.9:g.39735644C>G
IFNL4 RefSeqGene	NG_055295.1:g.8853G>C
IFNL3 RefSeqGene (LRG_1011)	NG_042193.1:g.4968G>C
GRCh38.p14 chr 19 fix patch HG2569_PATCH	NW_025791808.1:g.25387C>G

Gene: IFNL3, interferon lambda 3 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
IFNL3 transcript variant 1	NM_001346937.2:c.11-35G>C	N/A	Intron Variant
IFNL3 transcript variant 2	NM_172139.4:c.-37=	N/A	5 Prime UTR 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
GRCh38.p14 chr 19	NC_000019.10:g.39245004=	NC_000019.10:g.39245004C>G
GRCh37.p13 chr 19	NC_000019.9:g.39735644=	NC_000019.9:g.39735644C>G
IFNL4 RefSeqGene	NG_055295.1:g.8853=	NG_055295.1:g.8853G>C
IFNL3 RefSeqGene (LRG_1011)	NG_042193.1:g.4968=	NG_042193.1:g.4968G>C
IFNL3 transcript variant 2	NM_172139.4:c.-37=	NM_172139.4:c.-37G>C
IFNL3 transcript variant 2	NM_172139.3:c.-37=	NM_172139.3:c.-37G>C
GRCh38.p14 chr 19 fix patch HG2569_PATCH	NW_025791808.1:g.25387=	NW_025791808.1:g.25387C>G
IFNL3 transcript variant 1	NM_001346937.2:c.11-35=	NM_001346937.2:c.11-35G>C
IFNL3 transcript variant X1	XM_005258765.1:c.11-35=	XM_005258765.1:c.11-35G>C

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#.

59 SubSNP, 17 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss3607898	Dec 03, 2013 (138)
2	WI_SSAHASNP	ss6629693	Sep 28, 2016 (149)
3	WI_SSAHASNP	ss12454920	Apr 01, 2015 (144)
4	SSAHASNP	ss35151364	May 24, 2005 (125)
5	HUMANGENOME_JCVI	ss96306168	Feb 06, 2009 (130)
6	ENSEMBL	ss139730465	Dec 01, 2009 (131)
7	BCM-HGSC-SUB	ss208505809	Jul 04, 2010 (132)
8	GMI	ss283208436	May 04, 2012 (137)
9	1000GENOMES	ss340458708	May 09, 2011 (134)
10	1000GENOMES	ss491158588	May 04, 2012 (137)
11	GSK-GENETICS	ss491256289	May 04, 2012 (137)
12	SSMP	ss661845334	Apr 25, 2013 (138)
13	NHLBI-ESP	ss713509835	Apr 25, 2013 (138)
14	EVA-GONL	ss994296006	Aug 21, 2014 (142)
15	1000GENOMES	ss1363150330	Aug 21, 2014 (142)
16	DDI	ss1428402817	Apr 01, 2015 (144)
17	EVA_EXAC	ss1693589542	Apr 01, 2015 (144)
18	EVA_MGP	ss1711512533	Apr 01, 2015 (144)
19	HAMMER_LAB	ss1809306048	Sep 08, 2015 (146)
20	WEILL_CORNELL_DGM	ss1937789839	Feb 12, 2016 (147)
21	ILLUMINA	ss1959863214	Feb 12, 2016 (147)
22	GRF	ss2702824659	Nov 08, 2017 (151)
23	GNOMAD	ss2743976049	Nov 08, 2017 (151)
24	GNOMAD	ss2750181941	Nov 08, 2017 (151)
25	GNOMAD	ss2962823858	Nov 08, 2017 (151)
26	SWEGEN	ss3017465647	Nov 08, 2017 (151)
27	ILLUMINA	ss3021904976	Nov 08, 2017 (151)
28	CSHL	ss3352301416	Nov 08, 2017 (151)
29	OMUKHERJEE_ADBS	ss3646536328	Oct 12, 2018 (152)
30	URBANLAB	ss3650917412	Oct 12, 2018 (152)
31	ILLUMINA	ss3652330910	Oct 12, 2018 (152)
32	ILLUMINA	ss3725728308	Jul 13, 2019 (153)
33	ACPOP	ss3743035963	Jul 13, 2019 (153)
34	EVA	ss3756060592	Jul 13, 2019 (153)
35	KHV_HUMAN_GENOMES	ss3821308630	Jul 13, 2019 (153)
36	EVA	ss3825285712	Apr 27, 2020 (154)
37	EVA	ss3841352625	Apr 27, 2020 (154)
38	EVA	ss3846858469	Apr 27, 2020 (154)
39	SGDP_PRJ	ss3888208999	Apr 27, 2020 (154)
40	KRGDB	ss3938319779	Apr 27, 2020 (154)
41	FSA-LAB	ss3984153807	Apr 27, 2021 (155)
42	EVA	ss3984742009	Apr 27, 2021 (155)
43	EVA	ss3986796471	Apr 27, 2021 (155)
44	TOPMED	ss5074710663	Apr 27, 2021 (155)
45	TOMMO_GENOMICS	ss5227741348	Apr 27, 2021 (155)
46	EVA	ss5237247231	Apr 27, 2021 (155)
47	1000G_HIGH_COVERAGE	ss5307234753	Oct 16, 2022 (156)
48	1000G_HIGH_COVERAGE	ss5612959386	Oct 16, 2022 (156)
49	EVA	ss5624090115	Oct 16, 2022 (156)
50	SANFORD_IMAGENETICS	ss5662384805	Oct 16, 2022 (156)
51	TOMMO_GENOMICS	ss5786368890	Oct 16, 2022 (156)
52	EVA	ss5800222771	Oct 16, 2022 (156)
53	YY_MCH	ss5817598762	Oct 16, 2022 (156)
54	EVA	ss5840544558	Oct 16, 2022 (156)
55	EVA	ss5848492239	Oct 16, 2022 (156)
56	EVA	ss5928090403	Oct 16, 2022 (156)
57	EVA	ss5936573837	Oct 16, 2022 (156)
58	EVA	ss5953799559	Oct 16, 2022 (156)
59	EVA	ss5979546198	Oct 16, 2022 (156)
60	1000Genomes	NC_000019.9 - 39735644	Oct 12, 2018 (152)
61	1000Genomes_30x	NC_000019.10 - 39245004	Oct 16, 2022 (156)
62	ExAC	NC_000019.9 - 39735644	Oct 12, 2018 (152)
63	gnomAD - Genomes	NC_000019.10 - 39245004	Apr 27, 2021 (155)
64	gnomAD - Exomes	NC_000019.9 - 39735644	Jul 13, 2019 (153)
65	GO Exome Sequencing Project	NC_000019.9 - 39735644	Oct 12, 2018 (152)
66	Genome of the Netherlands Release 5	NC_000019.9 - 39735644	Apr 27, 2020 (154)
67	KOREAN population from KRGDB	NC_000019.9 - 39735644	Apr 27, 2020 (154)
68	Medical Genome Project healthy controls from Spanish population	NC_000019.9 - 39735644	Apr 27, 2020 (154)
69	Northern Sweden	NC_000019.9 - 39735644	Jul 13, 2019 (153)
70	CNV burdens in cranial meningiomas	NC_000019.9 - 39735644	Apr 27, 2021 (155)
71	Qatari	NC_000019.9 - 39735644	Apr 27, 2020 (154)
72	SGDP_PRJ	NC_000019.9 - 39735644	Apr 27, 2020 (154)
73	8.3KJPN	NC_000019.9 - 39735644	Apr 27, 2021 (155)
74	14KJPN	NC_000019.10 - 39245004	Oct 16, 2022 (156)
75	TopMed	NC_000019.10 - 39245004	Apr 27, 2021 (155)
76	ALFA	NC_000019.10 - 39245004	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss35151364, ss208505809, ss283208436, ss491256289	NC_000019.8:44427483:C:G	NC_000019.10:39245003:C:G	(self)
76557189, 4093438, 13290395, 1742675, 18889811, 45497173, 628293, 16320828, 291564, 19831761, 40225979, 85710655, ss340458708, ss491158588, ss661845334, ss713509835, ss994296006, ss1363150330, ss1428402817, ss1693589542, ss1711512533, ss1809306048, ss1937789839, ss1959863214, ss2702824659, ss2743976049, ss2750181941, ss2962823858, ss3017465647, ss3021904976, ss3352301416, ss3646536328, ss3652330910, ss3743035963, ss3756060592, ss3825285712, ss3841352625, ss3888208999, ss3938319779, ss3984153807, ss3984742009, ss3986796471, ss5227741348, ss5624090115, ss5662384805, ss5800222771, ss5840544558, ss5848492239, ss5936573837, ss5953799559, ss5979546198	NC_000019.9:39735643:C:G	NC_000019.10:39245003:C:G	(self)
100485321, 539946185, 120205994, 290256327, 5785158777, ss3650917412, ss3725728308, ss3821308630, ss3846858469, ss5074710663, ss5237247231, ss5307234753, ss5612959386, ss5786368890, ss5817598762, ss5928090403	NC_000019.10:39245003:C:G	NC_000019.10:39245003:C:G	(self)
ss12454920	NT_011109.15:12003861:C:G	NC_000019.10:39245003:C:G	(self)
ss3607898, ss6629693, ss96306168, ss139730465	NT_011109.16:12003861:C:G	NC_000019.10:39245003:C:G	(self)

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

16 citations for rs28416813

PMID	Title	Author	Year	Journal
19749757	Genome-wide association of IL28B with response to pegylated interferon-alpha and ribavirin therapy for chronic hepatitis C.	Tanaka Y et al.	2009	Nature genetics
20950615	IL28B and the control of hepatitis C virus infection.	Balagopal A et al.	2010	Gastroenterology
21303914	Interferon lambdas: the next cytokine storm.	Kelly C et al.	2011	Gut
21346780	IL28B genetic variations are associated with high sustained virological response (SVR) of interferon-α plus ribavirin therapy in Taiwanese chronic HCV infection.	Chen JY et al.	2011	Genes and immunity
21360716	Estimating the net contribution of interleukin-28B variation to spontaneous hepatitis C virus clearance.	di Iulio J et al.	2011	Hepatology (Baltimore, Md.)
21479134	IL28B SNP rs12979860 is a critical predictor for on-treatment and sustained virologic response in patients with hepatitis C virus genotype-1 infection.	Lin CY et al.	2011	PloS one
21694902	New strategies for the treatment of hepatitis C virus infection and implications of resistance to new direct-acting antiviral agents.	Quer J et al.	2010	Infection and drug resistance
21820962	Interferon-lambda and therapy for chronic hepatitis C virus infection.	Donnelly RP et al.	2011	Trends in immunology
22046316	Genetic variation of the IL-28B promoter affecting gene expression.	Sugiyama M et al.	2011	PloS one
22162829	Evolutionary genetic dissection of human interferons.	Manry J et al.	2011	The Journal of experimental medicine
22214245	Genomics and proteomics in liver fibrosis and cirrhosis.	Hannivoort RA et al.	2012	Fibrogenesis & tissue repair
22253847	Sequence analysis of the IL28A/IL28B inverted gene duplication that contains polymorphisms associated with treatment response in hepatitis C patients.	Reynolds JM et al.	2012	PloS one
22295096	Genetic variations in IL28B and allergic disease in children.	Gaudieri S et al.	2012	PloS one
22328925	Deciphering the interleukin 28B variants that better predict response to pegylated interferon-α and ribavirin therapy in HCV/HIV-1 coinfected patients.	de Castellarnau M et al.	2012	PloS one
29705128	Identifying causal variants at the interferon lambda locus in case-control studies: Utilizing non-synonymous variant rs117648444 to probe the role of IFN-λ4.	Bhushan A et al.	2018	Gene
33725487	Functional genetic variants of the IFN-λ3 (IL28B) gene and transcription factor interactions on its promoter.	Roy S et al.	2021	Cytokine

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

rs28416813