Name: rs157292
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.

rs157292

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr5:156590079 (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: G=0.345019 (91323/264690, TOPMED)
G=0.330955 (46337/140010, GnomAD)
G=0.27395 (8454/30860, ALFA) (+ 16 more)
G=0.35629 (10068/28258, 14KJPN)
G=0.35603 (5967/16760, 8.3KJPN)
G=0.3659 (2343/6404, 1000G_30x)
G=0.3630 (1818/5008, 1000G)
G=0.2328 (1043/4480, Estonian)
G=0.2509 (967/3854, ALSPAC)
G=0.2430 (901/3708, TWINSUK)
G=0.3200 (937/2928, KOREAN)
G=0.244 (244/998, GoNL)
G=0.237 (142/600, NorthernSweden)
A=0.387 (120/310, SGDP_PRJ)
G=0.231 (50/216, Qatari)
G=0.236 (50/212, Vietnamese)
G=0.37 (33/90, HapMap)
G=0.30 (12/40, GENOME_DK)
A=0.32 (9/28, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: SGCD : 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	30860	A=0.72605	G=0.27395
European	Sub	24732	A=0.76128	G=0.23872
African	Sub	3168	A=0.4833	G=0.5167
African Others	Sub	124	A=0.371	G=0.629
African American	Sub	3044	A=0.4878	G=0.5122
Asian	Sub	128	A=0.656	G=0.344
East Asian	Sub	100	A=0.65	G=0.35
Other Asian	Sub	28	A=0.68	G=0.32
Latin American 1	Sub	168	A=0.720	G=0.280
Latin American 2	Sub	700	A=0.627	G=0.373
South Asian	Sub	114	A=0.684	G=0.316
Other	Sub	1850	A=0.7162	G=0.2838

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=0.654981	G=0.345019
gnomAD - Genomes	Global	Study-wide	140010	A=0.669045	G=0.330955
gnomAD - Genomes	European	Sub	75868	A=0.75940	G=0.24060
gnomAD - Genomes	African	Sub	41918	A=0.48790	G=0.51210
gnomAD - Genomes	American	Sub	13634	A=0.68226	G=0.31774
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	A=0.8222	G=0.1778
gnomAD - Genomes	East Asian	Sub	3112	A=0.6774	G=0.3226
gnomAD - Genomes	Other	Sub	2154	A=0.6797	G=0.3203
Allele Frequency Aggregator	Total	Global	30860	A=0.72605	G=0.27395
Allele Frequency Aggregator	European	Sub	24732	A=0.76128	G=0.23872
Allele Frequency Aggregator	African	Sub	3168	A=0.4833	G=0.5167
Allele Frequency Aggregator	Other	Sub	1850	A=0.7162	G=0.2838
Allele Frequency Aggregator	Latin American 2	Sub	700	A=0.627	G=0.373
Allele Frequency Aggregator	Latin American 1	Sub	168	A=0.720	G=0.280
Allele Frequency Aggregator	Asian	Sub	128	A=0.656	G=0.344
Allele Frequency Aggregator	South Asian	Sub	114	A=0.684	G=0.316
14KJPN	JAPANESE	Study-wide	28258	A=0.64371	G=0.35629
8.3KJPN	JAPANESE	Study-wide	16760	A=0.64397	G=0.35603
1000Genomes_30x	Global	Study-wide	6404	A=0.6341	G=0.3659
1000Genomes_30x	African	Sub	1786	A=0.4451	G=0.5549
1000Genomes_30x	Europe	Sub	1266	A=0.7457	G=0.2543
1000Genomes_30x	South Asian	Sub	1202	A=0.7363	G=0.2637
1000Genomes_30x	East Asian	Sub	1170	A=0.6932	G=0.3068
1000Genomes_30x	American	Sub	980	A=0.639	G=0.361
1000Genomes	Global	Study-wide	5008	A=0.6370	G=0.3630
1000Genomes	African	Sub	1322	A=0.4365	G=0.5635
1000Genomes	East Asian	Sub	1008	A=0.6925	G=0.3075
1000Genomes	Europe	Sub	1006	A=0.7475	G=0.2525
1000Genomes	South Asian	Sub	978	A=0.734	G=0.266
1000Genomes	American	Sub	694	A=0.641	G=0.359
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.7672	G=0.2328
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.7491	G=0.2509
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.7570	G=0.2430
KOREAN population from KRGDB	KOREAN	Study-wide	2928	A=0.6800	G=0.3200
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.756	G=0.244
Northern Sweden	ACPOP	Study-wide	600	A=0.763	G=0.237
SGDP_PRJ	Global	Study-wide	310	A=0.387	G=0.613
Qatari	Global	Study-wide	216	A=0.769	G=0.231
A Vietnamese Genetic Variation Database	Global	Study-wide	212	A=0.764	G=0.236
HapMap	Global	Study-wide	90	A=0.63	G=0.37
HapMap	Asian	Sub	90	A=0.63	G=0.37
The Danish reference pan genome	Danish	Study-wide	40	A=0.70	G=0.30
Siberian	Global	Study-wide	28	A=0.32	G=0.68

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 5	NC_000005.10:g.156590079A>G
GRCh37.p13 chr 5	NC_000005.9:g.156017089A>G
SGCD RefSeqGene (LRG_205)	NG_008693.2:g.724736A>G

Gene: SGCD, sarcoglycan delta (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SGCD transcript variant 1	NM_000337.6:c.382+761A>G	N/A	Intron Variant
SGCD transcript variant 3	NM_001128209.2:c.379+761A… NM_001128209.2:c.379+761A>G	N/A	Intron Variant
SGCD transcript variant 2	NM_172244.3:c.382+761A>G	N/A	Intron Variant
SGCD transcript variant X1	XM_005265966.6:c.382+761A… XM_005265966.6:c.382+761A>G	N/A	Intron Variant
SGCD transcript variant X6	XM_005265967.3:c.382+761A… XM_005265967.3:c.382+761A>G	N/A	Intron Variant
SGCD transcript variant X2	XM_017009724.2:c.382+761A… XM_017009724.2:c.382+761A>G	N/A	Intron Variant
SGCD transcript variant X3	XM_047417518.1:c.382+761A… XM_047417518.1:c.382+761A>G	N/A	Intron Variant
SGCD transcript variant X4	XM_047417519.1:c.382+761A… XM_047417519.1:c.382+761A>G	N/A	Intron Variant
SGCD transcript variant X5	XM_047417520.1:c.379+761A… XM_047417520.1:c.379+761A>G	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	A=	G
GRCh38.p14 chr 5	NC_000005.10:g.156590079=	NC_000005.10:g.156590079A>G
GRCh37.p13 chr 5	NC_000005.9:g.156017089=	NC_000005.9:g.156017089A>G
SGCD RefSeqGene (LRG_205)	NG_008693.2:g.724736=	NG_008693.2:g.724736A>G
SGCD transcript variant 1	NM_000337.5:c.382+761=	NM_000337.5:c.382+761A>G
SGCD transcript variant 1	NM_000337.6:c.382+761=	NM_000337.6:c.382+761A>G
SGCD transcript variant 3	NM_001128209.1:c.379+761=	NM_001128209.1:c.379+761A>G
SGCD transcript variant 3	NM_001128209.2:c.379+761=	NM_001128209.2:c.379+761A>G
SGCD transcript variant 2	NM_172244.2:c.382+761=	NM_172244.2:c.382+761A>G
SGCD transcript variant 2	NM_172244.3:c.382+761=	NM_172244.3:c.382+761A>G
SGCD transcript variant X1	XM_005265965.1:c.382+761=	XM_005265965.1:c.382+761A>G
SGCD transcript variant X2	XM_005265966.1:c.382+761=	XM_005265966.1:c.382+761A>G
SGCD transcript variant X1	XM_005265966.6:c.382+761=	XM_005265966.6:c.382+761A>G
SGCD transcript variant X4	XM_005265967.1:c.382+761=	XM_005265967.1:c.382+761A>G
SGCD transcript variant X6	XM_005265967.3:c.382+761=	XM_005265967.3:c.382+761A>G
SGCD transcript variant X2	XM_017009724.2:c.382+761=	XM_017009724.2:c.382+761A>G
SGCD transcript variant X3	XM_047417518.1:c.382+761=	XM_047417518.1:c.382+761A>G
SGCD transcript variant X4	XM_047417519.1:c.382+761=	XM_047417519.1:c.382+761A>G
SGCD transcript variant X5	XM_047417520.1:c.379+761=	XM_047417520.1:c.379+761A>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#.

79 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	KWOK	ss329532	Jul 12, 2000 (79)
2	KWOK	ss363814	Jul 12, 2000 (79)
3	SC_JCM	ss633507	Jul 16, 2000 (80)
4	KWOK	ss975909	Oct 04, 2000 (86)
5	KWOK	ss976874	Oct 04, 2000 (86)
6	KWOK	ss1690316	Oct 18, 2000 (87)
7	KWOK	ss1690614	Oct 18, 2000 (87)
8	SC_JCM	ss3407619	Sep 28, 2001 (100)
9	YUSUKE	ss4983955	Aug 28, 2002 (108)
10	CSHL-HAPMAP	ss17831897	Feb 27, 2004 (120)
11	ABI	ss44585979	Mar 14, 2006 (126)
12	HGSV	ss86086194	Dec 15, 2007 (130)
13	1000GENOMES	ss109542859	Jan 24, 2009 (130)
14	1000GENOMES	ss113511096	Jan 25, 2009 (130)
15	GMI	ss156221208	Dec 01, 2009 (131)
16	COMPLETE_GENOMICS	ss166010226	Jul 04, 2010 (132)
17	BUSHMAN	ss201076671	Jul 04, 2010 (132)
18	1000GENOMES	ss222059744	Jul 14, 2010 (132)
19	1000GENOMES	ss233215138	Jul 14, 2010 (132)
20	1000GENOMES	ss240324447	Jul 15, 2010 (132)
21	BL	ss253903507	May 09, 2011 (134)
22	GMI	ss278547149	May 04, 2012 (137)
23	PJP	ss293501084	May 09, 2011 (134)
24	ILLUMINA	ss481643543	May 04, 2012 (137)
25	ILLUMINA	ss484968649	May 04, 2012 (137)
26	ILLUMINA	ss534343447	Sep 08, 2015 (146)
27	TISHKOFF	ss558822153	Apr 25, 2013 (138)
28	SSMP	ss652727651	Apr 25, 2013 (138)
29	ILLUMINA	ss779895941	Sep 08, 2015 (146)
30	ILLUMINA	ss781532889	Sep 08, 2015 (146)
31	ILLUMINA	ss835373683	Sep 08, 2015 (146)
32	EVA-GONL	ss982301415	Aug 21, 2014 (142)
33	1000GENOMES	ss1317911856	Aug 21, 2014 (142)
34	DDI	ss1430553562	Apr 01, 2015 (144)
35	EVA_GENOME_DK	ss1581419810	Apr 01, 2015 (144)
36	EVA_DECODE	ss1591838527	Apr 01, 2015 (144)
37	EVA_UK10K_ALSPAC	ss1614387924	Apr 01, 2015 (144)
38	EVA_UK10K_TWINSUK	ss1657381957	Apr 01, 2015 (144)
39	HAMMER_LAB	ss1804155759	Sep 08, 2015 (146)
40	WEILL_CORNELL_DGM	ss1925555857	Feb 12, 2016 (147)
41	GENOMED	ss1970248092	Jul 19, 2016 (147)
42	JJLAB	ss2023388099	Sep 14, 2016 (149)
43	USC_VALOUEV	ss2151547069	Dec 20, 2016 (150)
44	HUMAN_LONGEVITY	ss2279611627	Dec 20, 2016 (150)
45	SYSTEMSBIOZJU	ss2626182463	Nov 08, 2017 (151)
46	ILLUMINA	ss2634362331	Nov 08, 2017 (151)
47	GRF	ss2707118912	Nov 08, 2017 (151)
48	GNOMAD	ss2832764224	Nov 08, 2017 (151)
49	SWEGEN	ss2998071412	Nov 08, 2017 (151)
50	BIOINF_KMB_FNS_UNIBA	ss3025476217	Nov 08, 2017 (151)
51	CSHL	ss3346704580	Nov 08, 2017 (151)
52	ILLUMINA	ss3629380927	Oct 12, 2018 (152)
53	ILLUMINA	ss3632284595	Oct 12, 2018 (152)
54	ILLUMINA	ss3642455028	Oct 12, 2018 (152)
55	EGCUT_WGS	ss3665995249	Jul 13, 2019 (153)
56	EVA_DECODE	ss3716040814	Jul 13, 2019 (153)
57	ACPOP	ss3732964036	Jul 13, 2019 (153)
58	EVA	ss3764278305	Jul 13, 2019 (153)
59	KHV_HUMAN_GENOMES	ss3807444949	Jul 13, 2019 (153)
60	EVA	ss3829589924	Apr 26, 2020 (154)
61	EVA	ss3838268367	Apr 26, 2020 (154)
62	EVA	ss3843711752	Apr 26, 2020 (154)
63	SGDP_PRJ	ss3863335568	Apr 26, 2020 (154)
64	KRGDB	ss3910022292	Apr 26, 2020 (154)
65	TOPMED	ss4684781970	Apr 26, 2021 (155)
66	TOMMO_GENOMICS	ss5174928923	Apr 26, 2021 (155)
67	1000G_HIGH_COVERAGE	ss5266450459	Oct 13, 2022 (156)
68	EVA	ss5315098647	Oct 13, 2022 (156)
69	EVA	ss5362083204	Oct 13, 2022 (156)
70	HUGCELL_USP	ss5464352717	Oct 13, 2022 (156)
71	EVA	ss5508272631	Oct 13, 2022 (156)
72	1000G_HIGH_COVERAGE	ss5551411405	Oct 13, 2022 (156)
73	SANFORD_IMAGENETICS	ss5639225658	Oct 13, 2022 (156)
74	TOMMO_GENOMICS	ss5712234305	Oct 13, 2022 (156)
75	YY_MCH	ss5806914541	Oct 13, 2022 (156)
76	EVA	ss5835878577	Oct 13, 2022 (156)
77	EVA	ss5855087497	Oct 13, 2022 (156)
78	EVA	ss5897028951	Oct 13, 2022 (156)
79	EVA	ss5967711788	Oct 13, 2022 (156)
80	1000Genomes	NC_000005.9 - 156017089	Oct 12, 2018 (152)
81	1000Genomes_30x	NC_000005.10 - 156590079	Oct 13, 2022 (156)
82	The Avon Longitudinal Study of Parents and Children	NC_000005.9 - 156017089	Oct 12, 2018 (152)
83	Genetic variation in the Estonian population	NC_000005.9 - 156017089	Oct 12, 2018 (152)
84	The Danish reference pan genome	NC_000005.9 - 156017089	Apr 26, 2020 (154)
85	gnomAD - Genomes	NC_000005.10 - 156590079	Apr 26, 2021 (155)
86	Genome of the Netherlands Release 5	NC_000005.9 - 156017089	Apr 26, 2020 (154)
87	HapMap	NC_000005.10 - 156590079	Apr 26, 2020 (154)
88	KOREAN population from KRGDB	NC_000005.9 - 156017089	Apr 26, 2020 (154)
89	Northern Sweden	NC_000005.9 - 156017089	Jul 13, 2019 (153)
90	Qatari	NC_000005.9 - 156017089	Apr 26, 2020 (154)
91	SGDP_PRJ	NC_000005.9 - 156017089	Apr 26, 2020 (154)
92	Siberian	NC_000005.9 - 156017089	Apr 26, 2020 (154)
93	8.3KJPN	NC_000005.9 - 156017089	Apr 26, 2021 (155)
94	14KJPN	NC_000005.10 - 156590079	Oct 13, 2022 (156)
95	TopMed	NC_000005.10 - 156590079	Apr 26, 2021 (155)
96	UK 10K study - Twins	NC_000005.9 - 156017089	Oct 12, 2018 (152)
97	A Vietnamese Genetic Variation Database	NC_000005.9 - 156017089	Jul 13, 2019 (153)
98	ALFA	NC_000005.10 - 156590079	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).

Associated ID	History Updated (Build)
rs3797575	Oct 08, 2002 (108)
rs60970359	May 26, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss86086194, ss109542859, ss113511096, ss166010226, ss201076671, ss253903507, ss278547149, ss293501084, ss484968649, ss1591838527	NC_000005.8:155949666:A:G	NC_000005.10:156590078:A:G	(self)
29614802, 16482517, 11733497, 7584749, 7315982, 17199686, 6248901, 7597787, 15352548, 4063423, 32898230, 16482517, 3653246, ss222059744, ss233215138, ss240324447, ss481643543, ss534343447, ss558822153, ss652727651, ss779895941, ss781532889, ss835373683, ss982301415, ss1317911856, ss1430553562, ss1581419810, ss1614387924, ss1657381957, ss1804155759, ss1925555857, ss1970248092, ss2023388099, ss2151547069, ss2626182463, ss2634362331, ss2707118912, ss2832764224, ss2998071412, ss3346704580, ss3629380927, ss3632284595, ss3642455028, ss3665995249, ss3732964036, ss3764278305, ss3829589924, ss3838268367, ss3863335568, ss3910022292, ss5174928923, ss5315098647, ss5362083204, ss5508272631, ss5639225658, ss5835878577, ss5967711788	NC_000005.9:156017088:A:G	NC_000005.10:156590078:A:G	(self)
38937340, 209457197, 3004688, 46071409, 522159527, 14172155654, ss2279611627, ss3025476217, ss3716040814, ss3807444949, ss3843711752, ss4684781970, ss5266450459, ss5464352717, ss5551411405, ss5712234305, ss5806914541, ss5855087497, ss5897028951	NC_000005.10:156590078:A:G	NC_000005.10:156590078:A:G	(self)
ss17831897	NT_023133.11:826646:A:G	NC_000005.10:156590078:A:G	(self)
ss329532, ss363814, ss633507, ss975909, ss976874, ss1690316, ss1690614, ss3407619, ss4983955, ss44585979, ss156221208	NT_023133.13:828361:A:G	NC_000005.10:156590078: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 rs157292

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

rs157292