Name: rs823157
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.

rs823157

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:205796667 (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 / T>G
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.222532 (58902/264690, TOPMED)
T=0.208434 (29172/139958, GnomAD)
T=0.16329 (4614/28256, 14KJPN) (+ 16 more)
T=0.16485 (3114/18890, ALFA)
T=0.16539 (2772/16760, 8.3KJPN)
T=0.2831 (1813/6404, 1000G_30x)
T=0.2825 (1415/5008, 1000G)
T=0.1022 (458/4480, Estonian)
T=0.0939 (362/3854, ALSPAC)
T=0.0936 (347/3708, TWINSUK)
T=0.2061 (604/2930, KOREAN)
T=0.1998 (366/1832, Korea1K)
T=0.096 (96/998, GoNL)
T=0.132 (79/600, NorthernSweden)
T=0.163 (84/514, SGDP_PRJ)
T=0.297 (98/330, HapMap)
T=0.171 (37/216, Qatari)
T=0.15 (8/52, Siberian)
T=0.15 (6/40, GENOME_DK)

Clinical Significance: Reported in ClinVar
Gene : Consequence: SLC41A1 : 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=0.16485	A=0.83515
European	Sub	14286	T=0.10528	A=0.89472
African	Sub	2946	T=0.4338	A=0.5662
African Others	Sub	114	T=0.500	A=0.500
African American	Sub	2832	T=0.4311	A=0.5689
Asian	Sub	112	T=0.214	A=0.786
East Asian	Sub	86	T=0.21	A=0.79
Other Asian	Sub	26	T=0.23	A=0.77
Latin American 1	Sub	146	T=0.199	A=0.801
Latin American 2	Sub	610	T=0.189	A=0.811
South Asian	Sub	98	T=0.18	A=0.82
Other	Sub	692	T=0.211	A=0.789

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=0.222532	A=0.777468
gnomAD - Genomes	Global	Study-wide	139958	T=0.208434	A=0.791566
gnomAD - Genomes	European	Sub	75890	T=0.09879	A=0.90121
gnomAD - Genomes	African	Sub	41826	T=0.42180	A=0.57820
gnomAD - Genomes	American	Sub	13644	T=0.17612	A=0.82388
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	T=0.1664	A=0.8336
gnomAD - Genomes	East Asian	Sub	3122	T=0.2072	A=0.7928
gnomAD - Genomes	Other	Sub	2152	T=0.1998	A=0.8002
14KJPN	JAPANESE	Study-wide	28256	T=0.16329	A=0.83671
Allele Frequency Aggregator	Total	Global	18890	T=0.16485	A=0.83515
Allele Frequency Aggregator	European	Sub	14286	T=0.10528	A=0.89472
Allele Frequency Aggregator	African	Sub	2946	T=0.4338	A=0.5662
Allele Frequency Aggregator	Other	Sub	692	T=0.211	A=0.789
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.189	A=0.811
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.199	A=0.801
Allele Frequency Aggregator	Asian	Sub	112	T=0.214	A=0.786
Allele Frequency Aggregator	South Asian	Sub	98	T=0.18	A=0.82
8.3KJPN	JAPANESE	Study-wide	16760	T=0.16539	A=0.83461
1000Genomes_30x	Global	Study-wide	6404	T=0.2831	A=0.7169
1000Genomes_30x	African	Sub	1786	T=0.4950	A=0.5050
1000Genomes_30x	Europe	Sub	1266	T=0.1232	A=0.8768
1000Genomes_30x	South Asian	Sub	1202	T=0.2471	A=0.7529
1000Genomes_30x	East Asian	Sub	1170	T=0.2410	A=0.7590
1000Genomes_30x	American	Sub	980	T=0.198	A=0.802
1000Genomes	Global	Study-wide	5008	T=0.2825	A=0.7175
1000Genomes	African	Sub	1322	T=0.5008	A=0.4992
1000Genomes	East Asian	Sub	1008	T=0.2450	A=0.7550
1000Genomes	Europe	Sub	1006	T=0.1243	A=0.8757
1000Genomes	South Asian	Sub	978	T=0.248	A=0.752
1000Genomes	American	Sub	694	T=0.199	A=0.801
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.1022	A=0.8978
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.0939	A=0.9061
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.0936	A=0.9064
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.2061	A=0.7939, C=0.0000, G=0.0000
Korean Genome Project	KOREAN	Study-wide	1832	T=0.1998	A=0.8002
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.096	A=0.904
Northern Sweden	ACPOP	Study-wide	600	T=0.132	A=0.868
SGDP_PRJ	Global	Study-wide	514	T=0.163	A=0.837
HapMap	Global	Study-wide	330	T=0.297	A=0.703
HapMap	African	Sub	120	T=0.558	A=0.442
HapMap	American	Sub	120	T=0.108	A=0.892
HapMap	Asian	Sub	90	T=0.20	A=0.80
Qatari	Global	Study-wide	216	T=0.171	A=0.829
Siberian	Global	Study-wide	52	T=0.15	A=0.85
The Danish reference pan genome	Danish	Study-wide	40	T=0.15	A=0.85

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.205796667T>A
GRCh38.p14 chr 1	NC_000001.11:g.205796667T>C
GRCh38.p14 chr 1	NC_000001.11:g.205796667T>G
GRCh37.p13 chr 1	NC_000001.10:g.205765795T>A
GRCh37.p13 chr 1	NC_000001.10:g.205765795T>C
GRCh37.p13 chr 1	NC_000001.10:g.205765795T>G

Gene: SLC41A1, solute carrier family 41 member 1 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SLC41A1 transcript	NM_173854.6:c.1072+257A>T	N/A	Intron Variant
SLC41A1 transcript variant X1	XM_047416887.1:c.1072+257… XM_047416887.1:c.1072+257A>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.

Allele: A (allele ID: 1238308 )

ClinVar Accession	Disease Names	Clinical Significance
RCV001656738.2	not provided	Benign

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	G
GRCh38.p14 chr 1	NC_000001.11:g.205796667=	NC_000001.11:g.205796667T>A	NC_000001.11:g.205796667T>C	NC_000001.11:g.205796667T>G
GRCh37.p13 chr 1	NC_000001.10:g.205765795=	NC_000001.10:g.205765795T>A	NC_000001.10:g.205765795T>C	NC_000001.10:g.205765795T>G
SLC41A1 transcript	NM_173854.4:c.1072+257=	NM_173854.4:c.1072+257A>T	NM_173854.4:c.1072+257A>G	NM_173854.4:c.1072+257A>C
SLC41A1 transcript	NM_173854.6:c.1072+257=	NM_173854.6:c.1072+257A>T	NM_173854.6:c.1072+257A>G	NM_173854.6:c.1072+257A>C
SLC41A1 transcript variant X1	XM_005245069.1:c.1072+257=	XM_005245069.1:c.1072+257A>T	XM_005245069.1:c.1072+257A>G	XM_005245069.1:c.1072+257A>C
SLC41A1 transcript variant X1	XM_047416887.1:c.1072+257=	XM_047416887.1:c.1072+257A>T	XM_047416887.1:c.1072+257A>G	XM_047416887.1:c.1072+257A>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#.

87 SubSNP, 19 Frequency, 1 ClinVar submissions

No	Submitter	Submission ID	Date (Build)
1	KWOK	ss1104838	Oct 05, 2000 (86)
2	TSC-CSHL	ss1293434	Oct 05, 2000 (92)
3	KWOK	ss1606457	Oct 18, 2000 (87)
4	SC_JCM	ss2636439	Nov 09, 2000 (111)
5	WI_SSAHASNP	ss6850759	Feb 20, 2003 (113)
6	SC_SNP	ss13043431	Dec 05, 2003 (119)
7	PERLEGEN	ss23702539	Sep 20, 2004 (123)
8	ABI	ss41102272	Mar 13, 2006 (126)
9	PERLEGEN	ss68790476	May 16, 2007 (127)
10	KRIBB_YJKIM	ss80730026	Dec 14, 2007 (130)
11	BCMHGSC_JDW	ss87946222	Mar 23, 2008 (129)
12	HUMANGENOME_JCVI	ss99281081	Feb 04, 2009 (130)
13	BGI	ss106627006	Feb 04, 2009 (130)
14	1000GENOMES	ss108891636	Jan 23, 2009 (130)
15	1000GENOMES	ss111668059	Jan 25, 2009 (130)
16	ENSEMBL	ss138141999	Dec 01, 2009 (131)
17	ENSEMBL	ss139091778	Dec 01, 2009 (131)
18	GMI	ss156198525	Dec 01, 2009 (131)
19	COMPLETE_GENOMICS	ss164975917	Jul 04, 2010 (132)
20	COMPLETE_GENOMICS	ss165722384	Jul 04, 2010 (132)
21	COMPLETE_GENOMICS	ss167454210	Jul 04, 2010 (132)
22	BUSHMAN	ss199520711	Jul 04, 2010 (132)
23	BCM-HGSC-SUB	ss205131863	Jul 04, 2010 (132)
24	1000GENOMES	ss218842510	Jul 14, 2010 (132)
25	1000GENOMES	ss230871757	Jul 14, 2010 (132)
26	1000GENOMES	ss238490158	Jul 15, 2010 (132)
27	GMI	ss276188083	May 04, 2012 (137)
28	GMI	ss284215248	Apr 25, 2013 (138)
29	PJP	ss290719020	May 09, 2011 (134)
30	TISHKOFF	ss555081270	Apr 25, 2013 (138)
31	SSMP	ss648648372	Apr 25, 2013 (138)
32	EVA-GONL	ss976064232	Aug 21, 2014 (142)
33	JMKIDD_LAB	ss1068542772	Aug 21, 2014 (142)
34	1000GENOMES	ss1294348777	Aug 21, 2014 (142)
35	DDI	ss1426089252	Apr 01, 2015 (144)
36	EVA_GENOME_DK	ss1574626051	Apr 01, 2015 (144)
37	EVA_DECODE	ss1585459381	Apr 01, 2015 (144)
38	EVA_UK10K_ALSPAC	ss1601977248	Apr 01, 2015 (144)
39	EVA_UK10K_TWINSUK	ss1644971281	Apr 01, 2015 (144)
40	HAMMER_LAB	ss1795623900	Sep 08, 2015 (146)
41	WEILL_CORNELL_DGM	ss1919290466	Feb 12, 2016 (147)
42	GENOMED	ss1966954263	Jul 19, 2016 (147)
43	JJLAB	ss2020166218	Sep 14, 2016 (149)
44	ILLUMINA	ss2094786274	Dec 20, 2016 (150)
45	ILLUMINA	ss2094995767	Dec 20, 2016 (150)
46	USC_VALOUEV	ss2148195926	Dec 20, 2016 (150)
47	HUMAN_LONGEVITY	ss2169473780	Dec 20, 2016 (150)
48	SYSTEMSBIOZJU	ss2624592040	Nov 08, 2017 (151)
49	GRF	ss2698186516	Nov 08, 2017 (151)
50	ILLUMINA	ss2710692278	Nov 08, 2017 (151)
51	GNOMAD	ss2765366374	Nov 08, 2017 (151)
52	SWEGEN	ss2988326397	Nov 08, 2017 (151)
53	BIOINF_KMB_FNS_UNIBA	ss3023843256	Nov 08, 2017 (151)
54	CSHL	ss3343876889	Nov 08, 2017 (151)
55	URBANLAB	ss3646870374	Oct 11, 2018 (152)
56	ILLUMINA	ss3651515536	Oct 11, 2018 (152)
57	EGCUT_WGS	ss3656286695	Jul 12, 2019 (153)
58	EVA_DECODE	ss3688481939	Jul 12, 2019 (153)
59	ACPOP	ss3727796153	Jul 12, 2019 (153)
60	EVA	ss3747242101	Jul 12, 2019 (153)
61	PACBIO	ss3783668084	Jul 12, 2019 (153)
62	PACBIO	ss3789283590	Jul 12, 2019 (153)
63	PACBIO	ss3794155859	Jul 12, 2019 (153)
64	KHV_HUMAN_GENOMES	ss3800248707	Jul 12, 2019 (153)
65	EVA	ss3826605570	Apr 25, 2020 (154)
66	EVA	ss3836703337	Apr 25, 2020 (154)
67	EVA	ss3842114599	Apr 25, 2020 (154)
68	SGDP_PRJ	ss3850742175	Apr 25, 2020 (154)
69	KRGDB	ss3896039952	Apr 25, 2020 (154)
70	KOGIC	ss3946343142	Apr 25, 2020 (154)
71	TOPMED	ss4480917803	Apr 25, 2021 (155)
72	TOMMO_GENOMICS	ss5148092274	Apr 25, 2021 (155)
73	EVA	ss5237166059	Apr 25, 2021 (155)
74	1000G_HIGH_COVERAGE	ss5245533692	Oct 12, 2022 (156)
75	EVA	ss5324309159	Oct 12, 2022 (156)
76	HUGCELL_USP	ss5445998659	Oct 12, 2022 (156)
77	EVA	ss5506162302	Oct 12, 2022 (156)
78	1000G_HIGH_COVERAGE	ss5519496740	Oct 12, 2022 (156)
79	EVA	ss5624002278	Oct 12, 2022 (156)
80	SANFORD_IMAGENETICS	ss5627298582	Oct 12, 2022 (156)
81	TOMMO_GENOMICS	ss5675754345	Oct 12, 2022 (156)
82	YY_MCH	ss5801571841	Oct 12, 2022 (156)
83	EVA	ss5833157040	Oct 12, 2022 (156)
84	EVA	ss5849252563	Oct 12, 2022 (156)
85	EVA	ss5911670662	Oct 12, 2022 (156)
86	EVA	ss5939130022	Oct 12, 2022 (156)
87	EVA	ss5980010571	Oct 12, 2022 (156)
88	1000Genomes	NC_000001.10 - 205765795	Oct 11, 2018 (152)
89	1000Genomes_30x	NC_000001.11 - 205796667	Oct 12, 2022 (156)
90	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 205765795	Oct 11, 2018 (152)
91	Genetic variation in the Estonian population	NC_000001.10 - 205765795	Oct 11, 2018 (152)
92	The Danish reference pan genome	NC_000001.10 - 205765795	Apr 25, 2020 (154)
93	gnomAD - Genomes	NC_000001.11 - 205796667	Apr 25, 2021 (155)
94	Genome of the Netherlands Release 5	NC_000001.10 - 205765795	Apr 25, 2020 (154)
95	HapMap	NC_000001.11 - 205796667	Apr 25, 2020 (154)
96	KOREAN population from KRGDB	NC_000001.10 - 205765795	Apr 25, 2020 (154)
97	Korean Genome Project	NC_000001.11 - 205796667	Apr 25, 2020 (154)
98	Northern Sweden	NC_000001.10 - 205765795	Jul 12, 2019 (153)
99	Qatari	NC_000001.10 - 205765795	Apr 25, 2020 (154)
100	SGDP_PRJ	NC_000001.10 - 205765795	Apr 25, 2020 (154)
101	Siberian	NC_000001.10 - 205765795	Apr 25, 2020 (154)
102	8.3KJPN	NC_000001.10 - 205765795	Apr 25, 2021 (155)
103	14KJPN	NC_000001.11 - 205796667	Oct 12, 2022 (156)
104	TopMed	NC_000001.11 - 205796667	Apr 25, 2021 (155)
105	UK 10K study - Twins	NC_000001.10 - 205765795	Oct 11, 2018 (152)
106	ALFA	NC_000001.11 - 205796667	Apr 25, 2021 (155)
107	ClinVar	RCV001656738.2	Oct 12, 2022 (156)

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)
rs870623	Jan 18, 2001 (92)
rs1775149	Feb 20, 2003 (111)
rs4951264	Mar 31, 2003 (113)
rs16830354	Oct 07, 2004 (123)
rs57509148	May 23, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss87946222, ss108891636, ss111668059, ss164975917, ss165722384, ss167454210, ss199520711, ss205131863, ss276188083, ss284215248, ss290719020, ss1585459381	NC_000001.9:204032417:T:A	NC_000001.11:205796666:T:A	(self)
5192696, 2860549, 2024943, 1853692, 1249341, 3217346, 1081018, 1332396, 2759155, 712280, 6061581, 2860549, ss218842510, ss230871757, ss238490158, ss555081270, ss648648372, ss976064232, ss1068542772, ss1294348777, ss1426089252, ss1574626051, ss1601977248, ss1644971281, ss1795623900, ss1919290466, ss1966954263, ss2020166218, ss2094786274, ss2094995767, ss2148195926, ss2624592040, ss2698186516, ss2710692278, ss2765366374, ss2988326397, ss3343876889, ss3651515536, ss3656286695, ss3727796153, ss3747242101, ss3783668084, ss3789283590, ss3794155859, ss3826605570, ss3836703337, ss3850742175, ss3896039952, ss5148092274, ss5324309159, ss5506162302, ss5624002278, ss5627298582, ss5833157040, ss5939130022, ss5980010571	NC_000001.10:205765794:T:A	NC_000001.11:205796666:T:A	(self)
RCV001656738.2, 7022675, 37402978, 251215, 2721143, 9591449, 44524138, 2349669108, ss2169473780, ss3023843256, ss3646870374, ss3688481939, ss3800248707, ss3842114599, ss3946343142, ss4480917803, ss5237166059, ss5245533692, ss5445998659, ss5519496740, ss5675754345, ss5801571841, ss5849252563, ss5911670662	NC_000001.11:205796666:T:A	NC_000001.11:205796666:T:A	(self)
ss1104838, ss1293434, ss1606457, ss2636439, ss6850759, ss23702539, ss41102272, ss68790476, ss80730026, ss99281081, ss106627006, ss138141999, ss139091778, ss156198525	NT_004487.19:57254436:T:A	NC_000001.11:205796666:T:A	(self)
ss13043431	NT_034410.4:2192687:T:A	NC_000001.11:205796666:T:A	(self)
3217346, ss3896039952	NC_000001.10:205765794:T:C	NC_000001.11:205796666:T:C	(self)
3217346, ss3896039952	NC_000001.10:205765794:T:G	NC_000001.11:205796666:T: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 rs823157

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
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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

rs823157