Name: rs62082718
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.

rs62082718

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr17:69084989 (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: T>A / T>C
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.101209 (26789/264690, TOPMED)
A=0.104679 (14671/140152, GnomAD)
A=0.00007 (2/28258, 14KJPN) (+ 18 more)
A=0.13251 (3693/27870, ALFA)
A=0.00012 (2/16760, 8.3KJPN)
A=0.11272 (1466/13006, GO-ESP)
A=0.0631 (404/6404, 1000G_30x)
A=0.0643 (322/5008, 1000G)
A=0.1435 (643/4480, Estonian)
A=0.1437 (554/3854, ALSPAC)
A=0.1467 (544/3708, TWINSUK)
A=0.0003 (1/2920, KOREAN)
A=0.134 (134/998, GoNL)
A=0.127 (76/600, NorthernSweden)
A=0.159 (85/534, MGP)
A=0.089 (27/302, FINRISK)
A=0.144 (31/216, Qatari)
T=0.48 (32/66, SGDP_PRJ)
A=0.23 (9/40, GENOME_DK)
T=0.5 (1/2, Siberian)
A=0.5 (1/2, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ABCA6 : 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	27870	T=0.86749	A=0.13251
European	Sub	20342	T=0.84874	A=0.15126
African	Sub	3540	T=0.9548	A=0.0452
African Others	Sub	122	T=0.984	A=0.016
African American	Sub	3418	T=0.9538	A=0.0462
Asian	Sub	168	T=1.000	A=0.000
East Asian	Sub	112	T=1.000	A=0.000
Other Asian	Sub	56	T=1.00	A=0.00
Latin American 1	Sub	146	T=0.822	A=0.178
Latin American 2	Sub	610	T=0.892	A=0.108
South Asian	Sub	98	T=0.90	A=0.10
Other	Sub	2966	T=0.8806	A=0.1194

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	T=0.898791	A=0.101209
gnomAD - Genomes	Global	Study-wide	140152	T=0.895321	A=0.104679
gnomAD - Genomes	European	Sub	75892	T=0.85442	A=0.14558
gnomAD - Genomes	African	Sub	42012	T=0.96758	A=0.03242
gnomAD - Genomes	American	Sub	13652	T=0.88851	A=0.11149
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	T=0.8470	A=0.1530
gnomAD - Genomes	East Asian	Sub	3128	T=0.9981	A=0.0019
gnomAD - Genomes	Other	Sub	2148	T=0.8953	A=0.1047
14KJPN	JAPANESE	Study-wide	28258	T=0.99993	A=0.00007
Allele Frequency Aggregator	Total	Global	27870	T=0.86749	A=0.13251
Allele Frequency Aggregator	European	Sub	20342	T=0.84874	A=0.15126
Allele Frequency Aggregator	African	Sub	3540	T=0.9548	A=0.0452
Allele Frequency Aggregator	Other	Sub	2966	T=0.8806	A=0.1194
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.892	A=0.108
Allele Frequency Aggregator	Asian	Sub	168	T=1.000	A=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.822	A=0.178
Allele Frequency Aggregator	South Asian	Sub	98	T=0.90	A=0.10
8.3KJPN	JAPANESE	Study-wide	16760	T=0.99988	A=0.00012
GO Exome Sequencing Project	Global	Study-wide	13006	T=0.88728	A=0.11272
GO Exome Sequencing Project	European American	Sub	8600	T=0.8491	A=0.1509
GO Exome Sequencing Project	African American	Sub	4406	T=0.9619	A=0.0381
1000Genomes_30x	Global	Study-wide	6404	T=0.9369	A=0.0631
1000Genomes_30x	African	Sub	1786	T=0.9905	A=0.0095
1000Genomes_30x	Europe	Sub	1266	T=0.8325	A=0.1675
1000Genomes_30x	South Asian	Sub	1202	T=0.9243	A=0.0757
1000Genomes_30x	East Asian	Sub	1170	T=0.9949	A=0.0051
1000Genomes_30x	American	Sub	980	T=0.920	A=0.080
1000Genomes	Global	Study-wide	5008	T=0.9357	A=0.0643
1000Genomes	African	Sub	1322	T=0.9902	A=0.0098
1000Genomes	East Asian	Sub	1008	T=0.9940	A=0.0060
1000Genomes	Europe	Sub	1006	T=0.8320	A=0.1680
1000Genomes	South Asian	Sub	978	T=0.922	A=0.078
1000Genomes	American	Sub	694	T=0.916	A=0.084
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.8565	A=0.1435
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.8563	A=0.1437
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.8533	A=0.1467
KOREAN population from KRGDB	KOREAN	Study-wide	2920	T=0.9997	A=0.0003
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.866	A=0.134
Northern Sweden	ACPOP	Study-wide	600	T=0.873	A=0.127
Medical Genome Project healthy controls from Spanish population	Spanish controls	Study-wide	534	T=0.841	A=0.159
FINRISK	Finnish from FINRISK project	Study-wide	302	T=0.911	A=0.089
Qatari	Global	Study-wide	216	T=0.856	A=0.144
SGDP_PRJ	Global	Study-wide	66	T=0.48	A=0.52
The Danish reference pan genome	Danish	Study-wide	40	T=0.78	A=0.23
Siberian	Global	Study-wide	2	T=0.5	A=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 17	NC_000017.11:g.69084989T>A
GRCh38.p14 chr 17	NC_000017.11:g.69084989T>C
GRCh37.p13 chr 17	NC_000017.10:g.67081130T>A
GRCh37.p13 chr 17	NC_000017.10:g.67081130T>C

Gene: ABCA6, ATP binding cassette subfamily A member 6 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ABCA6 transcript	NM_080284.3:c.4184+39A>T	N/A	Intron Variant
ABCA6 transcript variant X1	XM_017024404.3:c.4184+39A… XM_017024404.3:c.4184+39A>T	N/A	Intron Variant
ABCA6 transcript variant X2	XM_017024405.3:c.4184+39A… XM_017024405.3:c.4184+39A>T	N/A	Intron Variant
ABCA6 transcript variant X3	XM_024450683.2:c.4184+39A… XM_024450683.2:c.4184+39A>T	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	T=	A	C
GRCh38.p14 chr 17	NC_000017.11:g.69084989=	NC_000017.11:g.69084989T>A	NC_000017.11:g.69084989T>C
GRCh37.p13 chr 17	NC_000017.10:g.67081130=	NC_000017.10:g.67081130T>A	NC_000017.10:g.67081130T>C
ABCA6 transcript	NM_080284.2:c.4184+39=	NM_080284.2:c.4184+39A>T	NM_080284.2:c.4184+39A>G
ABCA6 transcript	NM_080284.3:c.4184+39=	NM_080284.3:c.4184+39A>T	NM_080284.3:c.4184+39A>G
ABCA6 transcript variant X1	XM_017024404.3:c.4184+39=	XM_017024404.3:c.4184+39A>T	XM_017024404.3:c.4184+39A>G
ABCA6 transcript variant X2	XM_017024405.3:c.4184+39=	XM_017024405.3:c.4184+39A>T	XM_017024405.3:c.4184+39A>G
ABCA6 transcript variant X3	XM_024450683.2:c.4184+39=	XM_024450683.2:c.4184+39A>T	XM_024450683.2:c.4184+39A>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#.

63 SubSNP, 24 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	BCMHGSC_JDW	ss90646870	Mar 24, 2008 (129)
2	1000GENOMES	ss109885140	Jan 24, 2009 (130)
3	ENSEMBL	ss137162319	Dec 01, 2009 (131)
4	BUSHMAN	ss202725664	Jul 04, 2010 (132)
5	1000GENOMES	ss237304817	Jul 15, 2010 (132)
6	1000GENOMES	ss491130589	May 04, 2012 (137)
7	CLINSEQ_SNP	ss491742279	May 04, 2012 (137)
8	ILLUMINA	ss535776417	Sep 08, 2015 (146)
9	SSMP	ss661188951	Apr 25, 2013 (138)
10	NHLBI-ESP	ss713416089	Apr 25, 2013 (138)
11	EVA-GONL	ss993287139	Aug 21, 2014 (142)
12	JMKIDD_LAB	ss1067574333	Aug 21, 2014 (142)
13	JMKIDD_LAB	ss1081181324	Aug 21, 2014 (142)
14	1000GENOMES	ss1359361782	Aug 21, 2014 (142)
15	DDI	ss1428083741	Apr 01, 2015 (144)
16	EVA_GENOME_DK	ss1578225642	Apr 01, 2015 (144)
17	EVA_FINRISK	ss1584108165	Apr 01, 2015 (144)
18	EVA_UK10K_ALSPAC	ss1636010104	Apr 01, 2015 (144)
19	EVA_UK10K_TWINSUK	ss1679004137	Apr 01, 2015 (144)
20	EVA_EXAC	ss1692936362	Apr 01, 2015 (144)
21	EVA_EXAC	ss1692936363	Apr 01, 2015 (144)
22	EVA_DECODE	ss1697336061	Apr 01, 2015 (144)
23	EVA_MGP	ss1711470742	Apr 01, 2015 (144)
24	WEILL_CORNELL_DGM	ss1936748833	Feb 12, 2016 (147)
25	JJLAB	ss2029146264	Sep 14, 2016 (149)
26	USC_VALOUEV	ss2157629793	Dec 20, 2016 (150)
27	HUMAN_LONGEVITY	ss2218247112	Dec 20, 2016 (150)
28	GNOMAD	ss2742962857	Nov 08, 2017 (151)
29	GNOMAD	ss2749848673	Nov 08, 2017 (151)
30	GNOMAD	ss2951957417	Nov 08, 2017 (151)
31	SWEGEN	ss3015828872	Nov 08, 2017 (151)
32	BIOINF_KMB_FNS_UNIBA	ss3028395427	Nov 08, 2017 (151)
33	CSHL	ss3351819180	Nov 08, 2017 (151)
34	ILLUMINA	ss3627710264	Oct 12, 2018 (152)
35	OMUKHERJEE_ADBS	ss3646515593	Oct 12, 2018 (152)
36	EGCUT_WGS	ss3682693491	Jul 13, 2019 (153)
37	EVA_DECODE	ss3700822922	Jul 13, 2019 (153)
38	ACPOP	ss3742176103	Jul 13, 2019 (153)
39	EVA	ss3754876215	Jul 13, 2019 (153)
40	KHV_HUMAN_GENOMES	ss3820143013	Jul 13, 2019 (153)
41	EVA	ss3825146135	Apr 27, 2020 (154)
42	EVA	ss3825905526	Apr 27, 2020 (154)
43	EVA	ss3834954356	Apr 27, 2020 (154)
44	SGDP_PRJ	ss3886120099	Apr 27, 2020 (154)
45	KRGDB	ss3935881520	Apr 27, 2020 (154)
46	FSA-LAB	ss3984122007	Apr 27, 2021 (155)
47	EVA	ss3986739025	Apr 27, 2021 (155)
48	TOPMED	ss5042298925	Apr 27, 2021 (155)
49	TOMMO_GENOMICS	ss5223266845	Apr 27, 2021 (155)
50	1000G_HIGH_COVERAGE	ss5303771850	Oct 16, 2022 (156)
51	EVA	ss5428733726	Oct 16, 2022 (156)
52	HUGCELL_USP	ss5496750939	Oct 16, 2022 (156)
53	1000G_HIGH_COVERAGE	ss5607798945	Oct 16, 2022 (156)
54	EVA	ss5624075278	Oct 16, 2022 (156)
55	SANFORD_IMAGENETICS	ss5660452542	Oct 16, 2022 (156)
56	TOMMO_GENOMICS	ss5779748229	Oct 16, 2022 (156)
57	EVA	ss5800210999	Oct 16, 2022 (156)
58	YY_MCH	ss5816688797	Oct 16, 2022 (156)
59	EVA	ss5834224097	Oct 16, 2022 (156)
60	EVA	ss5848456670	Oct 16, 2022 (156)
61	EVA	ss5851876379	Oct 16, 2022 (156)
62	EVA	ss5914643086	Oct 16, 2022 (156)
63	EVA	ss5951849894	Oct 16, 2022 (156)
64	1000Genomes	NC_000017.10 - 67081130	Oct 12, 2018 (152)
65	1000Genomes_30x	NC_000017.11 - 69084989	Oct 16, 2022 (156)
66	The Avon Longitudinal Study of Parents and Children	NC_000017.10 - 67081130	Oct 12, 2018 (152)
67	Genetic variation in the Estonian population	NC_000017.10 - 67081130	Oct 12, 2018 (152)
68	ExAC Submission ignored due to conflicting rows: Row 3391873 (NC_000017.10:67081129:T:T 102419/115798, NC_000017.10:67081129:T:A 13379/115798) Row 3391874 (NC_000017.10:67081129:T:T 115797/115798, NC_000017.10:67081129:T:C 1/115798)	-	Oct 12, 2018 (152)
69	ExAC Submission ignored due to conflicting rows: Row 3391873 (NC_000017.10:67081129:T:T 102419/115798, NC_000017.10:67081129:T:A 13379/115798) Row 3391874 (NC_000017.10:67081129:T:T 115797/115798, NC_000017.10:67081129:T:C 1/115798)	-	Oct 12, 2018 (152)
70	FINRISK	NC_000017.10 - 67081130	Apr 27, 2020 (154)
71	The Danish reference pan genome	NC_000017.10 - 67081130	Apr 27, 2020 (154)
72	gnomAD - Genomes	NC_000017.11 - 69084989	Apr 27, 2021 (155)
73	gnomAD - Exomes Submission ignored due to conflicting rows: Row 12270463 (NC_000017.10:67081129:T:T 189637/213632, NC_000017.10:67081129:T:A 23995/213632) Row 12270464 (NC_000017.10:67081129:T:T 213631/213632, NC_000017.10:67081129:T:C 1/213632)	-	Jul 13, 2019 (153)
74	gnomAD - Exomes Submission ignored due to conflicting rows: Row 12270463 (NC_000017.10:67081129:T:T 189637/213632, NC_000017.10:67081129:T:A 23995/213632) Row 12270464 (NC_000017.10:67081129:T:T 213631/213632, NC_000017.10:67081129:T:C 1/213632)	-	Jul 13, 2019 (153)
75	GO Exome Sequencing Project	NC_000017.10 - 67081130	Oct 12, 2018 (152)
76	Genome of the Netherlands Release 5	NC_000017.10 - 67081130	Apr 27, 2020 (154)
77	KOREAN population from KRGDB	NC_000017.10 - 67081130	Apr 27, 2020 (154)
78	Medical Genome Project healthy controls from Spanish population	NC_000017.10 - 67081130	Apr 27, 2020 (154)
79	Northern Sweden	NC_000017.10 - 67081130	Jul 13, 2019 (153)
80	Qatari	NC_000017.10 - 67081130	Apr 27, 2020 (154)
81	SGDP_PRJ	NC_000017.10 - 67081130	Apr 27, 2020 (154)
82	Siberian	NC_000017.10 - 67081130	Apr 27, 2020 (154)
83	8.3KJPN	NC_000017.10 - 67081130	Apr 27, 2021 (155)
84	14KJPN	NC_000017.11 - 69084989	Oct 16, 2022 (156)
85	TopMed	NC_000017.11 - 69084989	Apr 27, 2021 (155)
86	UK 10K study - Twins	NC_000017.10 - 67081130	Oct 12, 2018 (152)
87	ALFA	NC_000017.11 - 69084989	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
ss90646870, ss109885140, ss202725664, ss491742279, ss1697336061	NC_000017.9:64592724:T:A	NC_000017.11:69084988:T:A	(self)
72631047, 40245912, 28431739, 104626, 4425149, 1603196, 17931564, 43058914, 586502, 15460968, 18790755, 38137079, 10146147, 81236152, 40245912, ss237304817, ss491130589, ss535776417, ss661188951, ss713416089, ss993287139, ss1067574333, ss1081181324, ss1359361782, ss1428083741, ss1578225642, ss1584108165, ss1636010104, ss1679004137, ss1692936362, ss1711470742, ss1936748833, ss2029146264, ss2157629793, ss2742962857, ss2749848673, ss2951957417, ss3015828872, ss3351819180, ss3627710264, ss3646515593, ss3682693491, ss3742176103, ss3754876215, ss3825146135, ss3825905526, ss3834954356, ss3886120099, ss3935881520, ss3984122007, ss3986739025, ss5223266845, ss5428733726, ss5624075278, ss5660452542, ss5800210999, ss5834224097, ss5848456670, ss5951849894	NC_000017.10:67081129:T:A	NC_000017.11:69084988:T:A	(self)
95324880, 512574879, 113585333, 257844587, 8887096450, ss2218247112, ss3028395427, ss3700822922, ss3820143013, ss5042298925, ss5303771850, ss5496750939, ss5607798945, ss5779748229, ss5816688797, ss5851876379, ss5914643086	NC_000017.11:69084988:T:A	NC_000017.11:69084988:T:A	(self)
ss137162319	NT_010783.15:32355281:T:A	NC_000017.11:69084988:T:A	(self)
ss1692936363, ss2742962857	NC_000017.10:67081129:T:C	NC_000017.11:69084988:T:C	(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 rs62082718

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

rs62082718