Name: rs1699235
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.

rs1699235

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr20:5861993 (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: A>G
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.261291 (69161/264690, TOPMED)
A=0.270785 (37925/140056, GnomAD)
A=0.33700 (9523/28258, 14KJPN) (+ 15 more)
A=0.28597 (5402/18890, ALFA)
A=0.33264 (5575/16760, 8.3KJPN)
A=0.2541 (1627/6404, 1000G_30x)
A=0.2570 (1287/5008, 1000G)
A=0.2964 (1328/4480, Estonian)
A=0.3025 (1166/3854, ALSPAC)
A=0.3158 (1171/3708, TWINSUK)
A=0.2102 (616/2930, KOREAN)
A=0.2052 (376/1832, Korea1K)
A=0.315 (314/998, GoNL)
A=0.283 (170/600, NorthernSweden)
A=0.199 (104/522, SGDP_PRJ)
A=0.301 (65/216, Qatari)
A=0.12 (6/52, Siberian)
A=0.38 (15/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: SHLD1 : 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	18890	A=0.28597	G=0.71403
European	Sub	14286	A=0.30708	G=0.69292
African	Sub	2946	A=0.2037	G=0.7963
African Others	Sub	114	A=0.149	G=0.851
African American	Sub	2832	A=0.2059	G=0.7941
Asian	Sub	112	A=0.205	G=0.795
East Asian	Sub	86	A=0.22	G=0.78
Other Asian	Sub	26	A=0.15	G=0.85
Latin American 1	Sub	146	A=0.219	G=0.781
Latin American 2	Sub	610	A=0.234	G=0.766
South Asian	Sub	98	A=0.40	G=0.60
Other	Sub	692	A=0.257	G=0.743

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	A=0.261291	G=0.738709
gnomAD - Genomes	Global	Study-wide	140056	A=0.270785	G=0.729215
gnomAD - Genomes	European	Sub	75850	A=0.30823	G=0.69177
gnomAD - Genomes	African	Sub	41952	A=0.20941	G=0.79059
gnomAD - Genomes	American	Sub	13652	A=0.25798	G=0.74202
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	A=0.2789	G=0.7211
gnomAD - Genomes	East Asian	Sub	3126	A=0.2274	G=0.7726
gnomAD - Genomes	Other	Sub	2152	A=0.2793	G=0.7207
14KJPN	JAPANESE	Study-wide	28258	A=0.33700	G=0.66300
Allele Frequency Aggregator	Total	Global	18890	A=0.28597	G=0.71403
Allele Frequency Aggregator	European	Sub	14286	A=0.30708	G=0.69292
Allele Frequency Aggregator	African	Sub	2946	A=0.2037	G=0.7963
Allele Frequency Aggregator	Other	Sub	692	A=0.257	G=0.743
Allele Frequency Aggregator	Latin American 2	Sub	610	A=0.234	G=0.766
Allele Frequency Aggregator	Latin American 1	Sub	146	A=0.219	G=0.781
Allele Frequency Aggregator	Asian	Sub	112	A=0.205	G=0.795
Allele Frequency Aggregator	South Asian	Sub	98	A=0.40	G=0.60
8.3KJPN	JAPANESE	Study-wide	16760	A=0.33264	G=0.66736
1000Genomes_30x	Global	Study-wide	6404	A=0.2541	G=0.7459
1000Genomes_30x	African	Sub	1786	A=0.1859	G=0.8141
1000Genomes_30x	Europe	Sub	1266	A=0.3223	G=0.6777
1000Genomes_30x	South Asian	Sub	1202	A=0.3286	G=0.6714
1000Genomes_30x	East Asian	Sub	1170	A=0.2368	G=0.7632
1000Genomes_30x	American	Sub	980	A=0.219	G=0.781
1000Genomes	Global	Study-wide	5008	A=0.2570	G=0.7430
1000Genomes	African	Sub	1322	A=0.1846	G=0.8154
1000Genomes	East Asian	Sub	1008	A=0.2411	G=0.7589
1000Genomes	Europe	Sub	1006	A=0.3131	G=0.6869
1000Genomes	South Asian	Sub	978	A=0.332	G=0.668
1000Genomes	American	Sub	694	A=0.231	G=0.769
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.2964	G=0.7036
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.3025	G=0.6975
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.3158	G=0.6842
KOREAN population from KRGDB	KOREAN	Study-wide	2930	A=0.2102	G=0.7898
Korean Genome Project	KOREAN	Study-wide	1832	A=0.2052	G=0.7948
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.315	G=0.685
Northern Sweden	ACPOP	Study-wide	600	A=0.283	G=0.717
SGDP_PRJ	Global	Study-wide	522	A=0.199	G=0.801
Qatari	Global	Study-wide	216	A=0.301	G=0.699
Siberian	Global	Study-wide	52	A=0.12	G=0.88
The Danish reference pan genome	Danish	Study-wide	40	A=0.38	G=0.62

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 20	NC_000020.11:g.5861993A>G
GRCh37.p13 chr 20	NC_000020.10:g.5842639A>G

Gene: SHLD1, shieldin complex subunit 1 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SHLD1 transcript variant 1	NM_001303477.2:c.179-1031… NM_001303477.2:c.179-1031A>G	N/A	Intron Variant
SHLD1 transcript variant 3	NM_001303478.2:c.83-1031A… NM_001303478.2:c.83-1031A>G	N/A	Intron Variant
SHLD1 transcript variant 2	NM_152504.4:c.179-1031A>G	N/A	Intron Variant
SHLD1 transcript variant 4	NM_001303479.2:c.	N/A	Genic Downstream Transcript Variant
SHLD1 transcript variant X2	XM_011529177.3:c.218-1031… XM_011529177.3:c.218-1031A>G	N/A	Intron Variant
SHLD1 transcript variant X1	XM_047439931.1:c.386-1031… XM_047439931.1:c.386-1031A>G	N/A	Intron Variant
SHLD1 transcript variant X3	XM_011529178.3:c.	N/A	Genic Downstream Transcript Variant
SHLD1 transcript variant X4	XM_011529180.3:c.	N/A	Genic Downstream Transcript Variant
SHLD1 transcript variant X5	XM_011529181.4:c.	N/A	Genic Downstream Transcript Variant
SHLD1 transcript variant X6	XM_011529182.3:c.	N/A	Genic Downstream 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	A=	G
GRCh38.p14 chr 20	NC_000020.11:g.5861993=	NC_000020.11:g.5861993A>G
GRCh37.p13 chr 20	NC_000020.10:g.5842639=	NC_000020.10:g.5842639A>G
SHLD1 transcript variant 1	NM_001303477.2:c.179-1031=	NM_001303477.2:c.179-1031A>G
SHLD1 transcript variant 3	NM_001303478.2:c.83-1031=	NM_001303478.2:c.83-1031A>G
C20orf196 transcript	NM_152504.2:c.179-1031=	NM_152504.2:c.179-1031A>G
SHLD1 transcript variant 2	NM_152504.4:c.179-1031=	NM_152504.4:c.179-1031A>G
SHLD1 transcript variant X2	XM_011529177.3:c.218-1031=	XM_011529177.3:c.218-1031A>G
SHLD1 transcript variant X1	XM_047439931.1:c.386-1031=	XM_047439931.1:c.386-1031A>G

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#.

78 SubSNP, 18 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss2532238	Nov 09, 2000 (89)
2	SC_SNP	ss8346421	Apr 21, 2003 (114)
3	BCM_SSAHASNP	ss10961873	Jul 11, 2003 (116)
4	WI_SSAHASNP	ss12489194	Jul 11, 2003 (116)
5	SSAHASNP	ss21771378	Apr 05, 2004 (121)
6	ABI	ss41395669	Mar 13, 2006 (126)
7	HGSV	ss78767331	Dec 06, 2007 (129)
8	BCMHGSC_JDW	ss91625894	Mar 24, 2008 (129)
9	HUMANGENOME_JCVI	ss96183632	Feb 05, 2009 (130)
10	BGI	ss103720437	Feb 23, 2009 (131)
11	1000GENOMES	ss111662231	Jan 25, 2009 (130)
12	1000GENOMES	ss115408542	Jan 25, 2009 (130)
13	ILLUMINA-UK	ss117469565	Feb 14, 2009 (130)
14	ENSEMBL	ss135681503	Dec 01, 2009 (131)
15	ENSEMBL	ss138204116	Dec 01, 2009 (131)
16	GMI	ss156120597	Dec 01, 2009 (131)
17	COMPLETE_GENOMICS	ss167740293	Jul 04, 2010 (132)
18	COMPLETE_GENOMICS	ss168973590	Jul 04, 2010 (132)
19	BUSHMAN	ss203819129	Jul 04, 2010 (132)
20	BCM-HGSC-SUB	ss208702481	Jul 04, 2010 (132)
21	1000GENOMES	ss228236269	Jul 14, 2010 (132)
22	1000GENOMES	ss237748730	Jul 15, 2010 (132)
23	1000GENOMES	ss243938240	Jul 15, 2010 (132)
24	BL	ss255458237	May 09, 2011 (134)
25	GMI	ss283287056	May 04, 2012 (137)
26	GMI	ss287416797	Apr 25, 2013 (138)
27	PJP	ss292602164	May 09, 2011 (134)
28	TISHKOFF	ss566113783	Apr 25, 2013 (138)
29	SSMP	ss661984749	Apr 25, 2013 (138)
30	EVA-GONL	ss994504119	Aug 21, 2014 (142)
31	JMKIDD_LAB	ss1082044708	Aug 21, 2014 (142)
32	1000GENOMES	ss1363936633	Aug 21, 2014 (142)
33	DDI	ss1428985531	Apr 01, 2015 (144)
34	EVA_GENOME_DK	ss1579422730	Apr 01, 2015 (144)
35	EVA_UK10K_ALSPAC	ss1638341354	Apr 01, 2015 (144)
36	EVA_UK10K_TWINSUK	ss1681335387	Apr 01, 2015 (144)
37	EVA_DECODE	ss1698558962	Apr 01, 2015 (144)
38	HAMMER_LAB	ss1809407182	Sep 08, 2015 (146)
39	WEILL_CORNELL_DGM	ss1938014506	Feb 12, 2016 (147)
40	GENOMED	ss1969082124	Jul 19, 2016 (147)
41	JJLAB	ss2029784883	Sep 14, 2016 (149)
42	USC_VALOUEV	ss2158339662	Dec 20, 2016 (150)
43	HUMAN_LONGEVITY	ss2241058875	Dec 20, 2016 (150)
44	SYSTEMSBIOZJU	ss2629389702	Nov 08, 2017 (151)
45	GRF	ss2704011996	Nov 08, 2017 (151)
46	GNOMAD	ss2965079437	Nov 08, 2017 (151)
47	SWEGEN	ss3017817036	Nov 08, 2017 (151)
48	BIOINF_KMB_FNS_UNIBA	ss3028724952	Nov 08, 2017 (151)
49	CSHL	ss3352403662	Nov 08, 2017 (151)
50	URBANLAB	ss3650963964	Oct 12, 2018 (152)
51	EGCUT_WGS	ss3684531019	Jul 13, 2019 (153)
52	EVA_DECODE	ss3706495929	Jul 13, 2019 (153)
53	ACPOP	ss3743220273	Jul 13, 2019 (153)
54	EVA	ss3758382309	Jul 13, 2019 (153)
55	PACBIO	ss3788590596	Jul 13, 2019 (153)
56	PACBIO	ss3793492113	Jul 13, 2019 (153)
57	PACBIO	ss3798379245	Jul 13, 2019 (153)
58	KHV_HUMAN_GENOMES	ss3821554449	Jul 13, 2019 (153)
59	EVA	ss3835570379	Apr 27, 2020 (154)
60	EVA	ss3841409376	Apr 27, 2020 (154)
61	EVA	ss3846916946	Apr 27, 2020 (154)
62	SGDP_PRJ	ss3888664585	Apr 27, 2020 (154)
63	KRGDB	ss3938851484	Apr 27, 2020 (154)
64	KOGIC	ss3981767040	Apr 27, 2020 (154)
65	TOPMED	ss5081155827	Apr 25, 2021 (155)
66	TOMMO_GENOMICS	ss5228703334	Apr 25, 2021 (155)
67	1000G_HIGH_COVERAGE	ss5307975275	Oct 13, 2022 (156)
68	EVA	ss5436053471	Oct 13, 2022 (156)
69	HUGCELL_USP	ss5500384977	Oct 13, 2022 (156)
70	EVA	ss5512145059	Oct 13, 2022 (156)
71	1000G_HIGH_COVERAGE	ss5613998503	Oct 13, 2022 (156)
72	SANFORD_IMAGENETICS	ss5662800018	Oct 13, 2022 (156)
73	TOMMO_GENOMICS	ss5787653462	Oct 13, 2022 (156)
74	YY_MCH	ss5817788614	Oct 13, 2022 (156)
75	EVA	ss5845399805	Oct 13, 2022 (156)
76	EVA	ss5853054163	Oct 13, 2022 (156)
77	EVA	ss5922544698	Oct 13, 2022 (156)
78	EVA	ss5957698332	Oct 13, 2022 (156)
79	1000Genomes	NC_000020.10 - 5842639	Oct 12, 2018 (152)
80	1000Genomes_30x	NC_000020.11 - 5861993	Oct 13, 2022 (156)
81	The Avon Longitudinal Study of Parents and Children	NC_000020.10 - 5842639	Oct 12, 2018 (152)
82	Genetic variation in the Estonian population	NC_000020.10 - 5842639	Oct 12, 2018 (152)
83	The Danish reference pan genome	NC_000020.10 - 5842639	Apr 27, 2020 (154)
84	gnomAD - Genomes	NC_000020.11 - 5861993	Apr 25, 2021 (155)
85	Genome of the Netherlands Release 5	NC_000020.10 - 5842639	Apr 27, 2020 (154)
86	KOREAN population from KRGDB	NC_000020.10 - 5842639	Apr 27, 2020 (154)
87	Korean Genome Project	NC_000020.11 - 5861993	Apr 27, 2020 (154)
88	Northern Sweden	NC_000020.10 - 5842639	Jul 13, 2019 (153)
89	Qatari	NC_000020.10 - 5842639	Apr 27, 2020 (154)
90	SGDP_PRJ	NC_000020.10 - 5842639	Apr 27, 2020 (154)
91	Siberian	NC_000020.10 - 5842639	Apr 27, 2020 (154)
92	8.3KJPN	NC_000020.10 - 5842639	Apr 25, 2021 (155)
93	14KJPN	NC_000020.11 - 5861993	Oct 13, 2022 (156)
94	TopMed	NC_000020.11 - 5861993	Apr 25, 2021 (155)
95	UK 10K study - Twins	NC_000020.10 - 5842639	Oct 12, 2018 (152)
96	ALFA	NC_000020.11 - 5861993	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)
rs74273698	Dec 02, 2009 (131)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss78767331, ss91625894, ss111662231, ss115408542, ss117469565, ss167740293, ss168973590, ss203819129, ss208702481, ss255458237, ss283287056, ss287416797, ss292602164, ss1698558962	NC_000020.9:5790638:A:G	NC_000020.11:5861992:A:G	(self)
77371662, 42827458, 30269267, 5587669, 19082909, 46028878, 16505138, 20056428, 40681565, 10856016, 86672641, 42827458, ss228236269, ss237748730, ss243938240, ss566113783, ss661984749, ss994504119, ss1082044708, ss1363936633, ss1428985531, ss1579422730, ss1638341354, ss1681335387, ss1809407182, ss1938014506, ss1969082124, ss2029784883, ss2158339662, ss2629389702, ss2704011996, ss2965079437, ss3017817036, ss3352403662, ss3684531019, ss3743220273, ss3758382309, ss3788590596, ss3793492113, ss3798379245, ss3835570379, ss3841409376, ss3888664585, ss3938851484, ss5228703334, ss5436053471, ss5512145059, ss5662800018, ss5845399805, ss5957698332	NC_000020.10:5842638:A:G	NC_000020.11:5861992:A:G	(self)
101524438, 545579520, 38145041, 121490566, 356264772, 3632701772, ss2241058875, ss3028724952, ss3650963964, ss3706495929, ss3821554449, ss3846916946, ss3981767040, ss5081155827, ss5307975275, ss5500384977, ss5613998503, ss5787653462, ss5817788614, ss5853054163, ss5922544698	NC_000020.11:5861992:A:G	NC_000020.11:5861992:A:G	(self)
ss2532238, ss8346421, ss10961873, ss12489194, ss21771378, ss41395669, ss96183632, ss103720437, ss135681503, ss138204116, ss156120597	NT_011387.8:5782638:A:G	NC_000020.11:5861992:A:G	(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 rs1699235

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

rs1699235