Name: rs6657985
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.

rs6657985

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:53001906 (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>C
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.155559 (41175/264690, TOPMED)
T=0.134453 (18846/140168, GnomAD)
T=0.31304 (8846/28258, 14KJPN) (+ 16 more)
T=0.10228 (1932/18890, ALFA)
T=0.31420 (5266/16760, 8.3KJPN)
T=0.2025 (1297/6404, 1000G_30x)
T=0.2009 (1006/5008, 1000G)
T=0.0533 (239/4480, Estonian)
T=0.0703 (271/3854, ALSPAC)
T=0.0739 (274/3708, TWINSUK)
T=0.3392 (994/2930, KOREAN)
T=0.3499 (641/1832, Korea1K)
T=0.053 (53/998, GoNL)
T=0.057 (34/600, NorthernSweden)
T=0.156 (75/482, SGDP_PRJ)
T=0.083 (18/216, Qatari)
T=0.297 (63/212, Vietnamese)
T=0.07 (4/54, Siberian)
T=0.07 (3/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: SCP2 : 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	T=0.10228	C=0.89772
European	Sub	14286	T=0.06258	C=0.93742
African	Sub	2946	T=0.2301	C=0.7699
African Others	Sub	114	T=0.237	C=0.763
African American	Sub	2832	T=0.2299	C=0.7701
Asian	Sub	112	T=0.312	C=0.688
East Asian	Sub	86	T=0.34	C=0.66
Other Asian	Sub	26	T=0.23	C=0.77
Latin American 1	Sub	146	T=0.116	C=0.884
Latin American 2	Sub	610	T=0.298	C=0.702
South Asian	Sub	98	T=0.17	C=0.83
Other	Sub	692	T=0.158	C=0.842

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").

Download

Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	T=0.155559	C=0.844441
gnomAD - Genomes	Global	Study-wide	140168	T=0.134453	C=0.865547
gnomAD - Genomes	European	Sub	75932	T=0.06374	C=0.93626
gnomAD - Genomes	African	Sub	41996	T=0.22481	C=0.77519
gnomAD - Genomes	American	Sub	13648	T=0.22736	C=0.77264
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	T=0.0569	C=0.9431
gnomAD - Genomes	East Asian	Sub	3124	T=0.3207	C=0.6793
gnomAD - Genomes	Other	Sub	2146	T=0.1263	C=0.8737
14KJPN	JAPANESE	Study-wide	28258	T=0.31304	C=0.68696
Allele Frequency Aggregator	Total	Global	18890	T=0.10228	C=0.89772
Allele Frequency Aggregator	European	Sub	14286	T=0.06258	C=0.93742
Allele Frequency Aggregator	African	Sub	2946	T=0.2301	C=0.7699
Allele Frequency Aggregator	Other	Sub	692	T=0.158	C=0.842
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.298	C=0.702
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.116	C=0.884
Allele Frequency Aggregator	Asian	Sub	112	T=0.312	C=0.688
Allele Frequency Aggregator	South Asian	Sub	98	T=0.17	C=0.83
8.3KJPN	JAPANESE	Study-wide	16760	T=0.31420	C=0.68580
1000Genomes_30x	Global	Study-wide	6404	T=0.2025	C=0.7975
1000Genomes_30x	African	Sub	1786	T=0.2279	C=0.7721
1000Genomes_30x	Europe	Sub	1266	T=0.0585	C=0.9415
1000Genomes_30x	South Asian	Sub	1202	T=0.1098	C=0.8902
1000Genomes_30x	East Asian	Sub	1170	T=0.3436	C=0.6564
1000Genomes_30x	American	Sub	980	T=0.288	C=0.712
1000Genomes	Global	Study-wide	5008	T=0.2009	C=0.7991
1000Genomes	African	Sub	1322	T=0.2247	C=0.7753
1000Genomes	East Asian	Sub	1008	T=0.3383	C=0.6617
1000Genomes	Europe	Sub	1006	T=0.0596	C=0.9404
1000Genomes	South Asian	Sub	978	T=0.111	C=0.889
1000Genomes	American	Sub	694	T=0.287	C=0.713
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.0533	C=0.9467
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.0703	C=0.9297
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.0739	C=0.9261
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.3392	C=0.6608
Korean Genome Project	KOREAN	Study-wide	1832	T=0.3499	C=0.6501
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.053	C=0.947
Northern Sweden	ACPOP	Study-wide	600	T=0.057	C=0.943
SGDP_PRJ	Global	Study-wide	482	T=0.156	C=0.844
Qatari	Global	Study-wide	216	T=0.083	C=0.917
A Vietnamese Genetic Variation Database	Global	Study-wide	212	T=0.297	C=0.703
Siberian	Global	Study-wide	54	T=0.07	C=0.93
The Danish reference pan genome	Danish	Study-wide	40	T=0.07	C=0.93

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.53001906T>C
GRCh37.p13 chr 1	NC_000001.10:g.53467578T>C
SCP2 RefSeqGene	NG_012211.1:g.79631T>C

Gene: SCP2, sterol carrier protein 2 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SCP2 transcript variant 7	NM_001193599.2:c.1010-129… NM_001193599.2:c.1010-12984T>C	N/A	Intron Variant
SCP2 transcript variant 6	NM_001193600.2:c.950-1298… NM_001193600.2:c.950-12984T>C	N/A	Intron Variant
SCP2 transcript variant 8	NM_001193617.2:c.839-1298… NM_001193617.2:c.839-12984T>C	N/A	Intron Variant
SCP2 transcript variant 1	NM_002979.5:c.1082-12984T… NM_002979.5:c.1082-12984T>C	N/A	Intron Variant
SCP2 transcript variant 3	NM_001007099.3:c.	N/A	Genic Upstream Transcript Variant
SCP2 transcript variant 4	NM_001007100.3:c.	N/A	Genic Upstream Transcript Variant
SCP2 transcript variant 5	NM_001007250.3:c.	N/A	Genic Upstream Transcript Variant
SCP2 transcript variant 2	NM_001007098.3:c.	N/A	Genic Downstream Transcript Variant
SCP2 transcript variant 9	NM_001330587.2:c.	N/A	Genic Downstream Transcript Variant
SCP2 transcript variant X2	XM_005271103.5:c.1082-129… XM_005271103.5:c.1082-12984T>C	N/A	Intron Variant
SCP2 transcript variant X5	XM_011541935.3:c.1082-882… XM_011541935.3:c.1082-882T>C	N/A	Intron Variant
SCP2 transcript variant X1	XM_047427504.1:c.1082-129… XM_047427504.1:c.1082-12984T>C	N/A	Intron Variant
SCP2 transcript variant X3	XM_047427506.1:c.1082-882… XM_047427506.1:c.1082-882T>C	N/A	Intron Variant
SCP2 transcript variant X4	XM_047427507.1:c.1082-882… XM_047427507.1:c.1082-882T>C	N/A	Intron Variant
SCP2 transcript variant X6	XM_047427508.1:c.950-882T… XM_047427508.1:c.950-882T>C	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=	C
GRCh38.p14 chr 1	NC_000001.11:g.53001906=	NC_000001.11:g.53001906T>C
GRCh37.p13 chr 1	NC_000001.10:g.53467578=	NC_000001.10:g.53467578T>C
SCP2 RefSeqGene	NG_012211.1:g.79631=	NG_012211.1:g.79631T>C
SCP2 transcript variant 7	NM_001193599.1:c.1010-12984=	NM_001193599.1:c.1010-12984T>C
SCP2 transcript variant 7	NM_001193599.2:c.1010-12984=	NM_001193599.2:c.1010-12984T>C
SCP2 transcript variant 6	NM_001193600.1:c.950-12984=	NM_001193600.1:c.950-12984T>C
SCP2 transcript variant 6	NM_001193600.2:c.950-12984=	NM_001193600.2:c.950-12984T>C
SCP2 transcript variant 8	NM_001193617.1:c.839-12984=	NM_001193617.1:c.839-12984T>C
SCP2 transcript variant 8	NM_001193617.2:c.839-12984=	NM_001193617.2:c.839-12984T>C
SCP2 transcript variant 1	NM_002979.4:c.1082-12984=	NM_002979.4:c.1082-12984T>C
SCP2 transcript variant 1	NM_002979.5:c.1082-12984=	NM_002979.5:c.1082-12984T>C
SCP2 transcript variant X1	XM_005271103.1:c.1082-12984=	XM_005271103.1:c.1082-12984T>C
SCP2 transcript variant X2	XM_005271103.5:c.1082-12984=	XM_005271103.5:c.1082-12984T>C
SCP2 transcript variant X5	XM_011541935.3:c.1082-882=	XM_011541935.3:c.1082-882T>C
SCP2 transcript variant X1	XM_047427504.1:c.1082-12984=	XM_047427504.1:c.1082-12984T>C
SCP2 transcript variant X3	XM_047427506.1:c.1082-882=	XM_047427506.1:c.1082-882T>C
SCP2 transcript variant X4	XM_047427507.1:c.1082-882=	XM_047427507.1:c.1082-882T>C
SCP2 transcript variant X6	XM_047427508.1:c.950-882=	XM_047427508.1:c.950-882T>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#.

76 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	BCM_SSAHASNP	ss9811495	Jul 11, 2003 (116)
2	SC_SNP	ss15397460	Feb 27, 2004 (120)
3	CSHL-HAPMAP	ss17328910	Feb 27, 2004 (120)
4	SSAHASNP	ss20492744	Apr 05, 2004 (121)
5	ABI	ss41139809	Mar 14, 2006 (126)
6	HGSV	ss80273803	Dec 15, 2007 (130)
7	BCMHGSC_JDW	ss87425445	Mar 23, 2008 (129)
8	HUMANGENOME_JCVI	ss97936350	Feb 05, 2009 (130)
9	1000GENOMES	ss110434063	Jan 24, 2009 (130)
10	ILLUMINA-UK	ss118685903	Dec 01, 2009 (131)
11	ENSEMBL	ss137932328	Dec 01, 2009 (131)
12	ENSEMBL	ss138945434	Dec 01, 2009 (131)
13	GMI	ss154983536	Dec 01, 2009 (131)
14	COMPLETE_GENOMICS	ss163378530	Jul 04, 2010 (132)
15	COMPLETE_GENOMICS	ss164266118	Jul 04, 2010 (132)
16	COMPLETE_GENOMICS	ss166502881	Jul 04, 2010 (132)
17	BUSHMAN	ss198437599	Jul 04, 2010 (132)
18	BCM-HGSC-SUB	ss205456116	Jul 04, 2010 (132)
19	1000GENOMES	ss218376404	Jul 14, 2010 (132)
20	1000GENOMES	ss230528367	Jul 14, 2010 (132)
21	1000GENOMES	ss238223551	Jul 15, 2010 (132)
22	BL	ss253088568	May 09, 2011 (134)
23	GMI	ss275820611	May 04, 2012 (137)
24	GMI	ss284047372	Apr 25, 2013 (138)
25	PJP	ss290508349	May 09, 2011 (134)
26	TISHKOFF	ss554095731	Apr 25, 2013 (138)
27	SSMP	ss647918683	Apr 25, 2013 (138)
28	EVA-GONL	ss975145102	Aug 21, 2014 (142)
29	JMKIDD_LAB	ss1067874484	Aug 21, 2014 (142)
30	1000GENOMES	ss1290834954	Aug 21, 2014 (142)
31	DDI	ss1425803229	Apr 01, 2015 (144)
32	EVA_GENOME_DK	ss1574048966	Apr 01, 2015 (144)
33	EVA_DECODE	ss1584510966	Apr 01, 2015 (144)
34	EVA_UK10K_ALSPAC	ss1600142906	Apr 01, 2015 (144)
35	EVA_UK10K_TWINSUK	ss1643136939	Apr 01, 2015 (144)
36	HAMMER_LAB	ss1794334723	Sep 08, 2015 (146)
37	WEILL_CORNELL_DGM	ss1918353621	Feb 12, 2016 (147)
38	GENOMED	ss1966741738	Jul 19, 2016 (147)
39	JJLAB	ss2019691457	Sep 14, 2016 (149)
40	USC_VALOUEV	ss2147705236	Dec 20, 2016 (150)
41	HUMAN_LONGEVITY	ss2162387425	Dec 20, 2016 (150)
42	SYSTEMSBIOZJU	ss2624358268	Nov 08, 2017 (151)
43	GRF	ss2697616839	Nov 08, 2017 (151)
44	GNOMAD	ss2754994912	Nov 08, 2017 (151)
45	SWEGEN	ss2986793765	Nov 08, 2017 (151)
46	BIOINF_KMB_FNS_UNIBA	ss3023606023	Nov 08, 2017 (151)
47	CSHL	ss3343446892	Nov 08, 2017 (151)
48	URBANLAB	ss3646659684	Oct 11, 2018 (152)
49	EGCUT_WGS	ss3654857138	Jul 12, 2019 (153)
50	EVA_DECODE	ss3686742647	Jul 12, 2019 (153)
51	ACPOP	ss3727033791	Jul 12, 2019 (153)
52	EVA	ss3746184627	Jul 12, 2019 (153)
53	PACBIO	ss3783404970	Jul 12, 2019 (153)
54	PACBIO	ss3789063638	Jul 12, 2019 (153)
55	PACBIO	ss3793936310	Jul 12, 2019 (153)
56	KHV_HUMAN_GENOMES	ss3799194576	Jul 12, 2019 (153)
57	EVA	ss3826163374	Apr 25, 2020 (154)
58	EVA	ss3836468780	Apr 25, 2020 (154)
59	EVA	ss3841874782	Apr 25, 2020 (154)
60	SGDP_PRJ	ss3848816035	Apr 25, 2020 (154)
61	KRGDB	ss3893822490	Apr 25, 2020 (154)
62	KOGIC	ss3944480615	Apr 25, 2020 (154)
63	TOPMED	ss4449263950	Apr 25, 2021 (155)
64	TOMMO_GENOMICS	ss5143886189	Apr 25, 2021 (155)
65	1000G_HIGH_COVERAGE	ss5242219655	Oct 17, 2022 (156)
66	HUGCELL_USP	ss5443286066	Oct 17, 2022 (156)
67	EVA	ss5505845425	Oct 17, 2022 (156)
68	1000G_HIGH_COVERAGE	ss5514472257	Oct 17, 2022 (156)
69	SANFORD_IMAGENETICS	ss5625500147	Oct 17, 2022 (156)
70	TOMMO_GENOMICS	ss5668639673	Oct 17, 2022 (156)
71	YY_MCH	ss5800582393	Oct 17, 2022 (156)
72	EVA	ss5831939015	Oct 17, 2022 (156)
73	EVA	ss5848898470	Oct 17, 2022 (156)
74	EVA	ss5908200824	Oct 17, 2022 (156)
75	EVA	ss5937330527	Oct 17, 2022 (156)
76	EVA	ss5979957412	Oct 17, 2022 (156)
77	1000Genomes	NC_000001.10 - 53467578	Oct 11, 2018 (152)
78	1000Genomes_30x	NC_000001.11 - 53001906	Oct 17, 2022 (156)
79	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 53467578	Oct 11, 2018 (152)
80	Genetic variation in the Estonian population	NC_000001.10 - 53467578	Oct 11, 2018 (152)
81	The Danish reference pan genome	NC_000001.10 - 53467578	Apr 25, 2020 (154)
82	gnomAD - Genomes	NC_000001.11 - 53001906	Apr 25, 2021 (155)
83	Genome of the Netherlands Release 5	NC_000001.10 - 53467578	Apr 25, 2020 (154)
84	KOREAN population from KRGDB	NC_000001.10 - 53467578	Apr 25, 2020 (154)
85	Korean Genome Project	NC_000001.11 - 53001906	Apr 25, 2020 (154)
86	Northern Sweden	NC_000001.10 - 53467578	Jul 12, 2019 (153)
87	Qatari	NC_000001.10 - 53467578	Apr 25, 2020 (154)
88	SGDP_PRJ	NC_000001.10 - 53467578	Apr 25, 2020 (154)
89	Siberian	NC_000001.10 - 53467578	Apr 25, 2020 (154)
90	8.3KJPN	NC_000001.10 - 53467578	Apr 25, 2021 (155)
91	14KJPN	NC_000001.11 - 53001906	Oct 17, 2022 (156)
92	TopMed	NC_000001.11 - 53001906	Apr 25, 2021 (155)
93	UK 10K study - Twins	NC_000001.10 - 53467578	Oct 11, 2018 (152)
94	A Vietnamese Genetic Variation Database	NC_000001.10 - 53467578	Jul 12, 2019 (153)
95	ALFA	NC_000001.11 - 53001906	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)
rs59990949	May 25, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss80273803	NC_000001.8:53179598:T:C	NC_000001.11:53001905:T:C	(self)
ss87425445, ss110434063, ss118685903, ss163378530, ss164266118, ss166502881, ss198437599, ss205456116, ss253088568, ss275820611, ss284047372, ss290508349, ss1584510966	NC_000001.9:53240165:T:C	NC_000001.11:53001905:T:C	(self)
1551347, 842983, 595386, 1495460, 357031, 999884, 318656, 395551, 833015, 221590, 1855496, 842983, 172206, ss218376404, ss230528367, ss238223551, ss554095731, ss647918683, ss975145102, ss1067874484, ss1290834954, ss1425803229, ss1574048966, ss1600142906, ss1643136939, ss1794334723, ss1918353621, ss1966741738, ss2019691457, ss2147705236, ss2624358268, ss2697616839, ss2754994912, ss2986793765, ss3343446892, ss3654857138, ss3727033791, ss3746184627, ss3783404970, ss3789063638, ss3793936310, ss3826163374, ss3836468780, ss3848816035, ss3893822490, ss5143886189, ss5505845425, ss5625500147, ss5831939015, ss5937330527, ss5979957412	NC_000001.10:53467577:T:C	NC_000001.11:53001905:T:C	(self)
1998192, 11003315, 858616, 2476777, 12870285, 1984644895, ss2162387425, ss3023606023, ss3646659684, ss3686742647, ss3799194576, ss3841874782, ss3944480615, ss4449263950, ss5242219655, ss5443286066, ss5514472257, ss5668639673, ss5800582393, ss5848898470, ss5908200824	NC_000001.11:53001905:T:C	NC_000001.11:53001905:T:C	(self)
ss9811495	NT_032977.5:5917314:T:C	NC_000001.11:53001905:T:C	(self)
ss15397460, ss17328910, ss20492744	NT_032977.6:15030648:T:C	NC_000001.11:53001905:T:C	(self)
ss41139809, ss97936350, ss137932328, ss138945434, ss154983536	NT_032977.9:23439495:T:C	NC_000001.11:53001905: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 rs6657985

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

rs6657985