Name: rs56020456
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.

rs56020456

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:154619406 (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: G>C / G>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.208999 (55320/264690, TOPMED)
T=0.206014 (28844/140010, GnomAD)
T=0.17020 (6041/35494, ALFA) (+ 16 more)
T=0.14185 (4008/28256, 14KJPN)
T=0.14296 (2396/16760, 8.3KJPN)
T=0.2189 (1402/6404, 1000G_30x)
T=0.2214 (1109/5008, 1000G)
T=0.2719 (1218/4480, Estonian)
T=0.1993 (768/3854, ALSPAC)
T=0.2095 (777/3708, TWINSUK)
T=0.1863 (546/2930, KOREAN)
T=0.1769 (324/1832, Korea1K)
T=0.185 (185/998, GoNL)
T=0.208 (125/600, NorthernSweden)
G=0.392 (87/222, SGDP_PRJ)
T=0.255 (55/216, Qatari)
T=0.140 (30/214, Vietnamese)
T=0.17 (7/40, GENOME_DK)
G=0.42 (10/24, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ADAR : 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	35588	G=0.82969	C=0.00000, T=0.17031
European	Sub	28122	G=0.82007	C=0.00000, T=0.17993
African	Sub	4792	G=0.8744	C=0.0000, T=0.1256
African Others	Sub	168	G=0.863	C=0.000, T=0.137
African American	Sub	4624	G=0.8748	C=0.0000, T=0.1252
Asian	Sub	102	G=0.980	C=0.000, T=0.020
East Asian	Sub	80	G=0.97	C=0.00, T=0.03
Other Asian	Sub	22	G=1.00	C=0.00, T=0.00
Latin American 1	Sub	104	G=0.990	C=0.000, T=0.010
Latin American 2	Sub	428	G=0.951	C=0.000, T=0.049
South Asian	Sub	68	G=0.93	C=0.00, T=0.07
Other	Sub	1972	G=0.8124	C=0.0000, T=0.1876

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	G=0.791001	T=0.208999
gnomAD - Genomes	Global	Study-wide	140010	G=0.793986	T=0.206014
gnomAD - Genomes	European	Sub	75838	G=0.78850	T=0.21150
gnomAD - Genomes	African	Sub	41946	G=0.80778	T=0.19222
gnomAD - Genomes	American	Sub	13624	G=0.77033	T=0.22967
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	G=0.7951	T=0.2049
gnomAD - Genomes	East Asian	Sub	3128	G=0.8536	T=0.1464
gnomAD - Genomes	Other	Sub	2150	G=0.7800	T=0.2200
Allele Frequency Aggregator	Total	Global	35494	G=0.82980	C=0.00000, T=0.17020
Allele Frequency Aggregator	European	Sub	28046	G=0.82012	C=0.00000, T=0.17988
Allele Frequency Aggregator	African	Sub	4792	G=0.8744	C=0.0000, T=0.1256
Allele Frequency Aggregator	Other	Sub	1954	G=0.8132	C=0.0000, T=0.1868
Allele Frequency Aggregator	Latin American 2	Sub	428	G=0.951	C=0.000, T=0.049
Allele Frequency Aggregator	Latin American 1	Sub	104	G=0.990	C=0.000, T=0.010
Allele Frequency Aggregator	Asian	Sub	102	G=0.980	C=0.000, T=0.020
Allele Frequency Aggregator	South Asian	Sub	68	G=0.93	C=0.00, T=0.07
14KJPN	JAPANESE	Study-wide	28256	G=0.85815	T=0.14185
8.3KJPN	JAPANESE	Study-wide	16760	G=0.85704	T=0.14296
1000Genomes_30x	Global	Study-wide	6404	G=0.7811	T=0.2189
1000Genomes_30x	African	Sub	1786	G=0.8158	T=0.1842
1000Genomes_30x	Europe	Sub	1266	G=0.8073	T=0.1927
1000Genomes_30x	South Asian	Sub	1202	G=0.6473	T=0.3527
1000Genomes_30x	East Asian	Sub	1170	G=0.8615	T=0.1385
1000Genomes_30x	American	Sub	980	G=0.752	T=0.248
1000Genomes	Global	Study-wide	5008	G=0.7786	T=0.2214
1000Genomes	African	Sub	1322	G=0.8109	T=0.1891
1000Genomes	East Asian	Sub	1008	G=0.8591	T=0.1409
1000Genomes	Europe	Sub	1006	G=0.8101	T=0.1899
1000Genomes	South Asian	Sub	978	G=0.642	T=0.358
1000Genomes	American	Sub	694	G=0.746	T=0.254
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.7281	T=0.2719
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.8007	T=0.1993
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.7905	T=0.2095
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.8137	T=0.1863
Korean Genome Project	KOREAN	Study-wide	1832	G=0.8231	T=0.1769
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.815	T=0.185
Northern Sweden	ACPOP	Study-wide	600	G=0.792	T=0.208
SGDP_PRJ	Global	Study-wide	222	G=0.392	T=0.608
Qatari	Global	Study-wide	216	G=0.745	T=0.255
A Vietnamese Genetic Variation Database	Global	Study-wide	214	G=0.860	T=0.140
The Danish reference pan genome	Danish	Study-wide	40	G=0.82	T=0.17
Siberian	Global	Study-wide	24	G=0.42	T=0.58

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 1	NC_000001.11:g.154619406G>C
GRCh38.p14 chr 1	NC_000001.11:g.154619406G>T
GRCh37.p13 chr 1	NC_000001.10:g.154591882G>C
GRCh37.p13 chr 1	NC_000001.10:g.154591882G>T
ADAR RefSeqGene (LRG_1212)	NG_011844.2:g.17155C>G
ADAR RefSeqGene (LRG_1212)	NG_011844.2:g.17155C>A

Gene: ADAR, adenosine deaminase RNA specific (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ADAR transcript variant 4	NM_001025107.3:c.-871+844… NM_001025107.3:c.-871+8449C>G	N/A	Intron Variant
ADAR transcript variant 6	NM_001365045.1:c.42+8548C… NM_001365045.1:c.42+8548C>G	N/A	Intron Variant
ADAR transcript variant 7	NM_001365046.1:c.-735+854… NM_001365046.1:c.-735+8548C>G	N/A	Intron Variant
ADAR transcript variant 1	NM_001111.5:c.	N/A	Genic Upstream Transcript Variant
ADAR transcript variant 5	NM_001193495.2:c.	N/A	Genic Upstream Transcript Variant
ADAR transcript variant 8	NM_001365047.1:c.	N/A	Genic Upstream Transcript Variant
ADAR transcript variant 9	NM_001365048.1:c.	N/A	Genic Upstream Transcript Variant
ADAR transcript variant 10	NM_001365049.1:c.	N/A	Genic Upstream Transcript Variant
ADAR transcript variant 2	NM_015840.4:c.	N/A	Genic Upstream Transcript Variant
ADAR transcript variant 3	NM_015841.4:c.	N/A	Genic Upstream Transcript Variant
ADAR transcript variant X1	XM_011509061.3:c.-871+844… XM_011509061.3:c.-871+8449C>G	N/A	Intron Variant
ADAR transcript variant X2	XM_011509062.2:c.33+5657C… XM_011509062.2:c.33+5657C>G	N/A	Intron Variant
ADAR transcript variant X3	XM_047428340.1:c.42+8548C… XM_047428340.1:c.42+8548C>G	N/A	Intron Variant
ADAR transcript variant X4	XM_047428386.1:c.33+5657C… XM_047428386.1:c.33+5657C>G	N/A	Intron Variant
ADAR transcript variant X5	XM_047428405.1:c.	N/A	Genic Upstream Transcript Variant
ADAR transcript variant X6	XM_047428441.1:c.	N/A	Genic Upstream Transcript 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	G=	C	T
GRCh38.p14 chr 1	NC_000001.11:g.154619406=	NC_000001.11:g.154619406G>C	NC_000001.11:g.154619406G>T
GRCh37.p13 chr 1	NC_000001.10:g.154591882=	NC_000001.10:g.154591882G>C	NC_000001.10:g.154591882G>T
ADAR RefSeqGene (LRG_1212)	NG_011844.2:g.17155=	NG_011844.2:g.17155C>G	NG_011844.2:g.17155C>A
ADAR transcript variant 4	NM_001025107.2:c.-871+8449=	NM_001025107.2:c.-871+8449C>G	NM_001025107.2:c.-871+8449C>A
ADAR transcript variant 4	NM_001025107.3:c.-871+8449=	NM_001025107.3:c.-871+8449C>G	NM_001025107.3:c.-871+8449C>A
ADAR transcript variant 6	NM_001365045.1:c.42+8548=	NM_001365045.1:c.42+8548C>G	NM_001365045.1:c.42+8548C>A
ADAR transcript variant 7	NM_001365046.1:c.-735+8548=	NM_001365046.1:c.-735+8548C>G	NM_001365046.1:c.-735+8548C>A
ADAR transcript variant X1	XM_011509061.3:c.-871+8449=	XM_011509061.3:c.-871+8449C>G	XM_011509061.3:c.-871+8449C>A
ADAR transcript variant X2	XM_011509062.2:c.33+5657=	XM_011509062.2:c.33+5657C>G	XM_011509062.2:c.33+5657C>A
ADAR transcript variant X3	XM_047428340.1:c.42+8548=	XM_047428340.1:c.42+8548C>G	XM_047428340.1:c.42+8548C>A
ADAR transcript variant X4	XM_047428386.1:c.33+5657=	XM_047428386.1:c.33+5657C>G	XM_047428386.1:c.33+5657C>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#.

76 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	HGSV	ss79004251	Dec 07, 2007 (129)
2	BCMHGSC_JDW	ss87824792	Mar 23, 2008 (130)
3	BGI	ss102785624	Dec 01, 2009 (131)
4	1000GENOMES	ss108599609	Jan 23, 2009 (130)
5	ILLUMINA-UK	ss119032435	Feb 15, 2009 (130)
6	ENSEMBL	ss138083371	Dec 01, 2009 (131)
7	COMPLETE_GENOMICS	ss165220788	Jul 04, 2010 (132)
8	BUSHMAN	ss199086733	Jul 04, 2010 (132)
9	1000GENOMES	ss218651401	Jul 14, 2010 (132)
10	1000GENOMES	ss230732049	Jul 14, 2010 (132)
11	1000GENOMES	ss238379940	Jul 15, 2010 (132)
12	GMI	ss276051339	May 04, 2012 (137)
13	GMI	ss284152713	Apr 25, 2013 (138)
14	PJP	ss290637138	May 09, 2011 (134)
15	ILLUMINA	ss482106563	May 04, 2012 (137)
16	ILLUMINA	ss483175401	May 04, 2012 (137)
17	ILLUMINA	ss535396534	Sep 08, 2015 (146)
18	TISHKOFF	ss554694053	Apr 25, 2013 (138)
19	SSMP	ss648414167	Apr 25, 2013 (138)
20	ILLUMINA	ss780179143	Sep 08, 2015 (146)
21	ILLUMINA	ss782031004	Sep 08, 2015 (146)
22	ILLUMINA	ss835663301	Sep 08, 2015 (146)
23	EVA-GONL	ss975682829	Aug 21, 2014 (142)
24	JMKIDD_LAB	ss1068269825	Aug 21, 2014 (142)
25	1000GENOMES	ss1292926668	Aug 21, 2014 (142)
26	DDI	ss1425979058	Apr 01, 2015 (144)
27	EVA_GENOME_DK	ss1574392269	Apr 01, 2015 (144)
28	EVA_DECODE	ss1585064281	Apr 01, 2015 (144)
29	EVA_UK10K_ALSPAC	ss1601214609	Apr 01, 2015 (144)
30	EVA_UK10K_TWINSUK	ss1644208642	Apr 01, 2015 (144)
31	WEILL_CORNELL_DGM	ss1918916735	Feb 12, 2016 (147)
32	JJLAB	ss2019973914	Sep 14, 2016 (149)
33	USC_VALOUEV	ss2147998438	Dec 20, 2016 (150)
34	HUMAN_LONGEVITY	ss2166543423	Dec 20, 2016 (150)
35	SYSTEMSBIOZJU	ss2624494993	Nov 08, 2017 (151)
36	ILLUMINA	ss2632576117	Nov 08, 2017 (151)
37	GRF	ss2697971357	Nov 08, 2017 (151)
38	GNOMAD	ss2761318995	Nov 08, 2017 (151)
39	AFFY	ss2984879334	Nov 08, 2017 (151)
40	AFFY	ss2985525109	Nov 08, 2017 (151)
41	SWEGEN	ss2987752547	Nov 08, 2017 (151)
42	BIOINF_KMB_FNS_UNIBA	ss3023744143	Nov 08, 2017 (151)
43	CSHL	ss3343710662	Nov 08, 2017 (151)
44	ILLUMINA	ss3626208510	Oct 11, 2018 (152)
45	ILLUMINA	ss3630609008	Oct 11, 2018 (152)
46	ILLUMINA	ss3641616667	Oct 11, 2018 (152)
47	ILLUMINA	ss3653648529	Oct 11, 2018 (152)
48	EGCUT_WGS	ss3655692758	Jul 12, 2019 (153)
49	EVA_DECODE	ss3687782923	Jul 12, 2019 (153)
50	ACPOP	ss3727485967	Jul 12, 2019 (153)
51	EVA	ss3746808445	Jul 12, 2019 (153)
52	PACBIO	ss3783566407	Jul 12, 2019 (153)
53	PACBIO	ss3789197935	Jul 12, 2019 (153)
54	PACBIO	ss3794069941	Jul 12, 2019 (153)
55	KHV_HUMAN_GENOMES	ss3799810115	Jul 12, 2019 (153)
56	EVA	ss3826424299	Apr 25, 2020 (154)
57	EVA	ss3836606748	Apr 25, 2020 (154)
58	EVA	ss3842015972	Apr 25, 2020 (154)
59	SGDP_PRJ	ss3850007089	Apr 25, 2020 (154)
60	KRGDB	ss3895213608	Apr 25, 2020 (154)
61	KOGIC	ss3945651863	Apr 25, 2020 (154)
62	TOPMED	ss4468312260	Apr 25, 2021 (155)
63	TOMMO_GENOMICS	ss5146484501	Apr 25, 2021 (155)
64	1000G_HIGH_COVERAGE	ss5244293954	Oct 12, 2022 (156)
65	EVA	ss5314650995	Oct 12, 2022 (156)
66	EVA	ss5322051573	Oct 12, 2022 (156)
67	HUGCELL_USP	ss5444887338	Oct 12, 2022 (156)
68	EVA	ss5506029323	Oct 12, 2022 (156)
69	1000G_HIGH_COVERAGE	ss5517622562	Oct 12, 2022 (156)
70	SANFORD_IMAGENETICS	ss5626591932	Oct 12, 2022 (156)
71	TOMMO_GENOMICS	ss5673680557	Oct 12, 2022 (156)
72	YY_MCH	ss5801260368	Oct 12, 2022 (156)
73	EVA	ss5832665900	Oct 12, 2022 (156)
74	EVA	ss5849109043	Oct 12, 2022 (156)
75	EVA	ss5910246849	Oct 12, 2022 (156)
76	EVA	ss5938385833	Oct 12, 2022 (156)
77	1000Genomes	NC_000001.10 - 154591882	Oct 11, 2018 (152)
78	1000Genomes_30x	NC_000001.11 - 154619406	Oct 12, 2022 (156)
79	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 154591882	Oct 11, 2018 (152)
80	Genetic variation in the Estonian population	NC_000001.10 - 154591882	Oct 11, 2018 (152)
81	The Danish reference pan genome	NC_000001.10 - 154591882	Apr 25, 2020 (154)
82	gnomAD - Genomes	NC_000001.11 - 154619406	Apr 25, 2021 (155)
83	Genome of the Netherlands Release 5	NC_000001.10 - 154591882	Apr 25, 2020 (154)
84	KOREAN population from KRGDB	NC_000001.10 - 154591882	Apr 25, 2020 (154)
85	Korean Genome Project	NC_000001.11 - 154619406	Apr 25, 2020 (154)
86	Northern Sweden	NC_000001.10 - 154591882	Jul 12, 2019 (153)
87	Qatari	NC_000001.10 - 154591882	Apr 25, 2020 (154)
88	SGDP_PRJ	NC_000001.10 - 154591882	Apr 25, 2020 (154)
89	Siberian	NC_000001.10 - 154591882	Apr 25, 2020 (154)
90	8.3KJPN	NC_000001.10 - 154591882	Apr 25, 2021 (155)
91	14KJPN	NC_000001.11 - 154619406	Oct 12, 2022 (156)
92	TopMed	NC_000001.11 - 154619406	Apr 25, 2021 (155)
93	UK 10K study - Twins	NC_000001.10 - 154591882	Oct 11, 2018 (152)
94	A Vietnamese Genetic Variation Database	NC_000001.10 - 154591882	Jul 12, 2019 (153)
95	ALFA	NC_000001.11 - 154619406	Apr 25, 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)
rs61811389	May 25, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
1498930360	NC_000001.11:154619405:G:C	NC_000001.11:154619405:G:C	(self)
ss79004251	NC_000001.8:151404954:G:T	NC_000001.11:154619405:G:T	(self)
ss87824792, ss108599609, ss119032435, ss165220788, ss199086733, ss276051339, ss284152713, ss290637138, ss482106563, ss1585064281	NC_000001.9:152858505:G:T	NC_000001.11:154619405:G:T	(self)
3718781, 2021933, 1431006, 1708755, 878464, 2391002, 770832, 958665, 2024069, 514792, 4453808, 2021933, 434531, ss218651401, ss230732049, ss238379940, ss483175401, ss535396534, ss554694053, ss648414167, ss780179143, ss782031004, ss835663301, ss975682829, ss1068269825, ss1292926668, ss1425979058, ss1574392269, ss1601214609, ss1644208642, ss1918916735, ss2019973914, ss2147998438, ss2624494993, ss2632576117, ss2697971357, ss2761318995, ss2984879334, ss2985525109, ss2987752547, ss3343710662, ss3626208510, ss3630609008, ss3641616667, ss3653648529, ss3655692758, ss3727485967, ss3746808445, ss3783566407, ss3789197935, ss3794069941, ss3826424299, ss3836606748, ss3850007089, ss3895213608, ss5146484501, ss5314650995, ss5322051573, ss5506029323, ss5626591932, ss5832665900, ss5938385833	NC_000001.10:154591881:G:T	NC_000001.11:154619405:G:T	(self)
5148497, 27059438, 2029864, 7517661, 31918595, 1498930360, ss2166543423, ss3023744143, ss3687782923, ss3799810115, ss3842015972, ss3945651863, ss4468312260, ss5244293954, ss5444887338, ss5517622562, ss5673680557, ss5801260368, ss5849109043, ss5910246849	NC_000001.11:154619405:G:T	NC_000001.11:154619405:G:T	(self)
ss102785624, ss138083371	NT_004487.19:6080523:G:T	NC_000001.11:154619405:G: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 rs56020456

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

rs56020456