Name: rs62064088
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.

rs62064088

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr17:17728701 (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=0.112460 (29767/264690, TOPMED)
T=0.097911 (13724/140168, GnomAD)
T=0.24168 (6829/28256, 14KJPN) (+ 16 more)
T=0.08613 (1627/18890, ALFA)
T=0.24230 (4061/16760, 8.3KJPN)
T=0.1505 (964/6404, 1000G_30x)
T=0.1516 (759/5008, 1000G)
T=0.0576 (258/4480, Estonian)
T=0.0919 (354/3854, ALSPAC)
T=0.0804 (298/3708, TWINSUK)
T=0.2857 (837/2930, KOREAN)
T=0.3035 (556/1832, Korea1K)
T=0.088 (88/998, GoNL)
T=0.070 (42/600, NorthernSweden)
T=0.069 (15/216, Qatari)
C=0.399 (75/188, SGDP_PRJ)
T=0.14 (10/72, Ancient Sardinia)
T=0.07 (3/40, GENOME_DK)
C=0.38 (6/16, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: RAI1 : 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	C=0.91387	T=0.08613
European	Sub	14286	C=0.92307	T=0.07693
African	Sub	2946	C=0.9036	T=0.0964
African Others	Sub	114	C=0.895	T=0.105
African American	Sub	2832	C=0.9040	T=0.0960
Asian	Sub	112	C=0.688	T=0.312
East Asian	Sub	86	C=0.70	T=0.30
Other Asian	Sub	26	C=0.65	T=0.35
Latin American 1	Sub	146	C=0.890	T=0.110
Latin American 2	Sub	610	C=0.808	T=0.192
South Asian	Sub	98	C=0.95	T=0.05
Other	Sub	692	C=0.897	T=0.103

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=0.887540	T=0.112460
gnomAD - Genomes	Global	Study-wide	140168	C=0.902089	T=0.097911
gnomAD - Genomes	European	Sub	75920	C=0.91791	T=0.08209
gnomAD - Genomes	African	Sub	42000	C=0.90514	T=0.09486
gnomAD - Genomes	American	Sub	13654	C=0.85440	T=0.14560
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	C=0.9239	T=0.0761
gnomAD - Genomes	East Asian	Sub	3118	C=0.6780	T=0.3220
gnomAD - Genomes	Other	Sub	2152	C=0.8778	T=0.1222
14KJPN	JAPANESE	Study-wide	28256	C=0.75832	T=0.24168
Allele Frequency Aggregator	Total	Global	18890	C=0.91387	T=0.08613
Allele Frequency Aggregator	European	Sub	14286	C=0.92307	T=0.07693
Allele Frequency Aggregator	African	Sub	2946	C=0.9036	T=0.0964
Allele Frequency Aggregator	Other	Sub	692	C=0.897	T=0.103
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.808	T=0.192
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.890	T=0.110
Allele Frequency Aggregator	Asian	Sub	112	C=0.688	T=0.312
Allele Frequency Aggregator	South Asian	Sub	98	C=0.95	T=0.05
8.3KJPN	JAPANESE	Study-wide	16760	C=0.75770	T=0.24230
1000Genomes_30x	Global	Study-wide	6404	C=0.8495	T=0.1505
1000Genomes_30x	African	Sub	1786	C=0.8869	T=0.1131
1000Genomes_30x	Europe	Sub	1266	C=0.9115	T=0.0885
1000Genomes_30x	South Asian	Sub	1202	C=0.9085	T=0.0915
1000Genomes_30x	East Asian	Sub	1170	C=0.6915	T=0.3085
1000Genomes_30x	American	Sub	980	C=0.817	T=0.183
1000Genomes	Global	Study-wide	5008	C=0.8484	T=0.1516
1000Genomes	African	Sub	1322	C=0.8873	T=0.1127
1000Genomes	East Asian	Sub	1008	C=0.6915	T=0.3085
1000Genomes	Europe	Sub	1006	C=0.9095	T=0.0905
1000Genomes	South Asian	Sub	978	C=0.916	T=0.084
1000Genomes	American	Sub	694	C=0.818	T=0.182
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.9424	T=0.0576
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.9081	T=0.0919
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.9196	T=0.0804
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.7143	G=0.0000, T=0.2857
Korean Genome Project	KOREAN	Study-wide	1832	C=0.6965	T=0.3035
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.912	T=0.088
Northern Sweden	ACPOP	Study-wide	600	C=0.930	T=0.070
Qatari	Global	Study-wide	216	C=0.931	T=0.069
SGDP_PRJ	Global	Study-wide	188	C=0.399	T=0.601
Ancient Sardinia genome-wide 1240k capture data generation and analysis	Global	Study-wide	72	C=0.86	T=0.14
The Danish reference pan genome	Danish	Study-wide	40	C=0.93	T=0.07
Siberian	Global	Study-wide	16	C=0.38	T=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 17	NC_000017.11:g.17728701C>G
GRCh38.p14 chr 17	NC_000017.11:g.17728701C>T
GRCh37.p13 chr 17	NC_000017.10:g.17632015C>G
GRCh37.p13 chr 17	NC_000017.10:g.17632015C>T
RAI1 RefSeqGene	NG_007101.2:g.52229C>G
RAI1 RefSeqGene	NG_007101.2:g.52229C>T

Gene: RAI1, retinoic acid induced 1 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
RAI1 transcript	NM_030665.4:c.-17+4542C>G	N/A	Intron Variant
RAI1 transcript variant X6	XM_017024027.2:c.-17+4542… XM_017024027.2:c.-17+4542C>G	N/A	Intron Variant
RAI1 transcript variant X5	XM_047435149.1:c.-17+4542… XM_047435149.1:c.-17+4542C>G	N/A	Intron Variant
RAI1 transcript variant X2	XM_047435151.1:c.-17+4542… XM_047435151.1:c.-17+4542C>G	N/A	Intron Variant
RAI1 transcript variant X3	XM_047435152.1:c.-17+4542… XM_047435152.1:c.-17+4542C>G	N/A	Intron Variant
RAI1 transcript variant X4	XM_047435153.1:c.-17+4690… XM_047435153.1:c.-17+46908C>G	N/A	Intron Variant
RAI1 transcript variant X1	XM_017024028.3:c.	N/A	Genic Upstream Transcript Variant
RAI1 transcript variant X7	XM_047435150.1: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	C=	G	T
GRCh38.p14 chr 17	NC_000017.11:g.17728701=	NC_000017.11:g.17728701C>G	NC_000017.11:g.17728701C>T
GRCh37.p13 chr 17	NC_000017.10:g.17632015=	NC_000017.10:g.17632015C>G	NC_000017.10:g.17632015C>T
RAI1 RefSeqGene	NG_007101.2:g.52229=	NG_007101.2:g.52229C>G	NG_007101.2:g.52229C>T
RAI1 transcript	NM_030665.3:c.-17+4542=	NM_030665.3:c.-17+4542C>G	NM_030665.3:c.-17+4542C>T
RAI1 transcript	NM_030665.4:c.-17+4542=	NM_030665.4:c.-17+4542C>G	NM_030665.4:c.-17+4542C>T
RAI1 transcript variant X6	XM_017024027.2:c.-17+4542=	XM_017024027.2:c.-17+4542C>G	XM_017024027.2:c.-17+4542C>T
RAI1 transcript variant X5	XM_047435149.1:c.-17+4542=	XM_047435149.1:c.-17+4542C>G	XM_047435149.1:c.-17+4542C>T
RAI1 transcript variant X2	XM_047435151.1:c.-17+4542=	XM_047435151.1:c.-17+4542C>G	XM_047435151.1:c.-17+4542C>T
RAI1 transcript variant X3	XM_047435152.1:c.-17+4542=	XM_047435152.1:c.-17+4542C>G	XM_047435152.1:c.-17+4542C>T
RAI1 transcript variant X4	XM_047435153.1:c.-17+46908=	XM_047435153.1:c.-17+46908C>G	XM_047435153.1:c.-17+46908C>T

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#.

47 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	BCMHGSC_JDW	ss90551413	Mar 24, 2008 (129)
2	ENSEMBL	ss137003284	Dec 01, 2009 (131)
3	GMI	ss157893689	Dec 01, 2009 (131)
4	1000GENOMES	ss227491438	Jul 14, 2010 (132)
5	1000GENOMES	ss237203025	Jul 15, 2010 (132)
6	1000GENOMES	ss243510460	Jul 15, 2010 (132)
7	GMI	ss282713366	May 04, 2012 (137)
8	SSMP	ss660994002	Apr 25, 2013 (138)
9	EVA-GONL	ss992979344	Aug 21, 2014 (142)
10	JMKIDD_LAB	ss1080974698	Aug 21, 2014 (142)
11	1000GENOMES	ss1358116633	Aug 21, 2014 (142)
12	EVA_GENOME_DK	ss1578112271	Apr 01, 2015 (144)
13	EVA_UK10K_ALSPAC	ss1635395745	Apr 01, 2015 (144)
14	EVA_UK10K_TWINSUK	ss1678389778	Apr 01, 2015 (144)
15	EVA_DECODE	ss1697021302	Apr 01, 2015 (144)
16	WEILL_CORNELL_DGM	ss1936431608	Feb 12, 2016 (147)
17	JJLAB	ss2029002331	Sep 14, 2016 (149)
18	USC_VALOUEV	ss2157454167	Dec 20, 2016 (150)
19	HUMAN_LONGEVITY	ss2215905160	Dec 20, 2016 (150)
20	GRF	ss2702002544	Nov 08, 2017 (151)
21	GNOMAD	ss2948286017	Nov 08, 2017 (151)
22	SWEGEN	ss3015286402	Nov 08, 2017 (151)
23	CSHL	ss3351678630	Nov 08, 2017 (151)
24	EGCUT_WGS	ss3682243594	Jul 13, 2019 (153)
25	EVA_DECODE	ss3700191410	Jul 13, 2019 (153)
26	ACPOP	ss3741921064	Jul 13, 2019 (153)
27	EVA	ss3754516281	Jul 13, 2019 (153)
28	KHV_HUMAN_GENOMES	ss3819790056	Jul 13, 2019 (153)
29	EVA	ss3834808536	Apr 27, 2020 (154)
30	SGDP_PRJ	ss3885456853	Apr 27, 2020 (154)
31	KRGDB	ss3935066317	Apr 27, 2020 (154)
32	KOGIC	ss3978513325	Apr 27, 2020 (154)
33	EVA	ss3985784950	Apr 26, 2021 (155)
34	TOPMED	ss5031192133	Apr 26, 2021 (155)
35	TOMMO_GENOMICS	ss5221740930	Apr 26, 2021 (155)
36	1000G_HIGH_COVERAGE	ss5302617973	Oct 16, 2022 (156)
37	EVA	ss5426721583	Oct 16, 2022 (156)
38	HUGCELL_USP	ss5495767529	Oct 16, 2022 (156)
39	EVA	ss5511737656	Oct 16, 2022 (156)
40	1000G_HIGH_COVERAGE	ss5606054077	Oct 16, 2022 (156)
41	SANFORD_IMAGENETICS	ss5659833206	Oct 16, 2022 (156)
42	TOMMO_GENOMICS	ss5777408141	Oct 16, 2022 (156)
43	YY_MCH	ss5816384922	Oct 16, 2022 (156)
44	EVA	ss5833796832	Oct 16, 2022 (156)
45	EVA	ss5851763958	Oct 16, 2022 (156)
46	EVA	ss5913432129	Oct 16, 2022 (156)
47	EVA	ss5951243775	Oct 16, 2022 (156)
48	1000Genomes	NC_000017.10 - 17632015	Oct 12, 2018 (152)
49	1000Genomes_30x	NC_000017.11 - 17728701	Oct 16, 2022 (156)
50	The Avon Longitudinal Study of Parents and Children	NC_000017.10 - 17632015	Oct 12, 2018 (152)
51	Genetic variation in the Estonian population	NC_000017.10 - 17632015	Oct 12, 2018 (152)
52	The Danish reference pan genome	NC_000017.10 - 17632015	Apr 27, 2020 (154)
53	gnomAD - Genomes	NC_000017.11 - 17728701	Apr 26, 2021 (155)
54	Genome of the Netherlands Release 5	NC_000017.10 - 17632015	Apr 27, 2020 (154)
55	KOREAN population from KRGDB	NC_000017.10 - 17632015	Apr 27, 2020 (154)
56	Korean Genome Project	NC_000017.11 - 17728701	Apr 27, 2020 (154)
57	Northern Sweden	NC_000017.10 - 17632015	Jul 13, 2019 (153)
58	Ancient Sardinia genome-wide 1240k capture data generation and analysis	NC_000017.10 - 17632015	Apr 26, 2021 (155)
59	Qatari	NC_000017.10 - 17632015	Apr 27, 2020 (154)
60	SGDP_PRJ	NC_000017.10 - 17632015	Apr 27, 2020 (154)
61	Siberian	NC_000017.10 - 17632015	Apr 27, 2020 (154)
62	8.3KJPN	NC_000017.10 - 17632015	Apr 26, 2021 (155)
63	14KJPN	NC_000017.11 - 17728701	Oct 16, 2022 (156)
64	TopMed	NC_000017.11 - 17728701	Apr 26, 2021 (155)
65	UK 10K study - Twins	NC_000017.10 - 17632015	Oct 12, 2018 (152)
66	ALFA	NC_000017.11 - 17728701	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
42243711, ss3935066317	NC_000017.10:17632014:C:G	NC_000017.11:17728700:C:G	(self)
ss90551413, ss282713366, ss1697021302	NC_000017.9:17572739:C:T	NC_000017.11:17728700:C:T	(self)
71338990, 39563729, 27981842, 4316254, 17638139, 42243711, 15205929, 1010877, 18473530, 37473833, 9970521, 79710237, 39563729, ss227491438, ss237203025, ss243510460, ss660994002, ss992979344, ss1080974698, ss1358116633, ss1578112271, ss1635395745, ss1678389778, ss1936431608, ss2029002331, ss2157454167, ss2702002544, ss2948286017, ss3015286402, ss3351678630, ss3682243594, ss3741921064, ss3754516281, ss3834808536, ss3885456853, ss3935066317, ss3985784950, ss5221740930, ss5426721583, ss5511737656, ss5659833206, ss5833796832, ss5951243775	NC_000017.10:17632014:C:T	NC_000017.11:17728700:C:T	(self)
93580012, 502949851, 34891326, 111245245, 246737795, 477114316, ss2215905160, ss3700191410, ss3819790056, ss3978513325, ss5031192133, ss5302617973, ss5495767529, ss5606054077, ss5777408141, ss5816384922, ss5851763958, ss5913432129	NC_000017.11:17728700:C:T	NC_000017.11:17728700:C:T	(self)
ss137003284, ss157893689	NT_010718.16:17235388:C:T	NC_000017.11:17728700: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 rs62064088

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

rs62064088