Name: rs830154
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.

rs830154

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr19:47435389 (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>A / C>G / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.042525 (11256/264690, TOPMED)
C=0.039119 (5477/140008, GnomAD)
C=0.01541 (465/30182, ALFA) (+ 14 more)
C=0.00025 (7/28258, 14KJPN)
C=0.00000 (0/16760, 8.3KJPN)
C=0.0475 (304/6404, 1000G_30x)
C=0.0443 (222/5008, 1000G)
C=0.0000 (0/3854, ALSPAC)
C=0.0000 (0/3708, TWINSUK)
C=0.0003 (1/2930, KOREAN)
C=0.0000 (0/1832, Korea1K)
C=0.000 (0/600, NorthernSweden)
C=0.018 (10/554, SGDP_PRJ)
C=0.037 (8/216, Qatari)
C=0.000 (0/212, Vietnamese)
C=0.00 (0/56, Siberian)
C=0.00 (0/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: SLC8A2 : 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	30182	C=0.01541	A=0.98459
European	Sub	24700	C=0.00049	A=0.99951
African	Sub	3168	C=0.1326	A=0.8674
African Others	Sub	124	C=0.161	A=0.839
African American	Sub	3044	C=0.1314	A=0.8686
Asian	Sub	128	C=0.000	A=1.000
East Asian	Sub	100	C=0.00	A=1.00
Other Asian	Sub	28	C=0.00	A=1.00
Latin American 1	Sub	168	C=0.042	A=0.958
Latin American 2	Sub	700	C=0.009	A=0.991
South Asian	Sub	114	C=0.000	A=1.000
Other	Sub	1204	C=0.0166	A=0.9834

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=0.042525	A=0.957475
gnomAD - Genomes	Global	Study-wide	140008	C=0.039119	A=0.960881
gnomAD - Genomes	European	Sub	75892	C=0.00047	A=0.99953
gnomAD - Genomes	African	Sub	41890	C=0.12318	A=0.87682
gnomAD - Genomes	American	Sub	13620	C=0.01601	A=0.98399
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	C=0.0000	A=1.0000
gnomAD - Genomes	East Asian	Sub	3130	C=0.0000	A=1.0000
gnomAD - Genomes	Other	Sub	2152	C=0.0293	A=0.9707
Allele Frequency Aggregator	Total	Global	30182	C=0.01541	A=0.98459
Allele Frequency Aggregator	European	Sub	24700	C=0.00049	A=0.99951
Allele Frequency Aggregator	African	Sub	3168	C=0.1326	A=0.8674
Allele Frequency Aggregator	Other	Sub	1204	C=0.0166	A=0.9834
Allele Frequency Aggregator	Latin American 2	Sub	700	C=0.009	A=0.991
Allele Frequency Aggregator	Latin American 1	Sub	168	C=0.042	A=0.958
Allele Frequency Aggregator	Asian	Sub	128	C=0.000	A=1.000
Allele Frequency Aggregator	South Asian	Sub	114	C=0.000	A=1.000
14KJPN	JAPANESE	Study-wide	28258	C=0.00025	A=0.99975
8.3KJPN	JAPANESE	Study-wide	16760	C=0.00000	A=1.00000
1000Genomes_30x	Global	Study-wide	6404	C=0.0475	A=0.9525
1000Genomes_30x	African	Sub	1786	C=0.1545	A=0.8455
1000Genomes_30x	Europe	Sub	1266	C=0.0008	A=0.9992
1000Genomes_30x	South Asian	Sub	1202	C=0.0000	A=1.0000
1000Genomes_30x	East Asian	Sub	1170	C=0.0000	A=1.0000
1000Genomes_30x	American	Sub	980	C=0.028	A=0.972
1000Genomes	Global	Study-wide	5008	C=0.0443	A=0.9557
1000Genomes	African	Sub	1322	C=0.1528	A=0.8472
1000Genomes	East Asian	Sub	1008	C=0.0000	A=1.0000
1000Genomes	Europe	Sub	1006	C=0.0020	A=0.9980
1000Genomes	South Asian	Sub	978	C=0.000	A=1.000
1000Genomes	American	Sub	694	C=0.026	A=0.974
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.0000	A=1.0000
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.0000	A=1.0000
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.0003	A=0.9997, G=0.0000, T=0.0000
Korean Genome Project	KOREAN	Study-wide	1832	C=0.0000	A=1.0000
Northern Sweden	ACPOP	Study-wide	600	C=0.000	A=1.000
SGDP_PRJ	Global	Study-wide	554	C=0.018	A=0.982
Qatari	Global	Study-wide	216	C=0.037	A=0.963
A Vietnamese Genetic Variation Database	Global	Study-wide	212	C=0.000	A=1.000
Siberian	Global	Study-wide	56	C=0.00	A=1.00
The Danish reference pan genome	Danish	Study-wide	40	C=0.00	A=1.00

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 19	NC_000019.10:g.47435389C>A
GRCh38.p14 chr 19	NC_000019.10:g.47435389C>G
GRCh38.p14 chr 19	NC_000019.10:g.47435389C>T
GRCh37.p13 chr 19	NC_000019.9:g.47938646C>A
GRCh37.p13 chr 19	NC_000019.9:g.47938646C>G
GRCh37.p13 chr 19	NC_000019.9:g.47938646C>T

Gene: SLC8A2, solute carrier family 8 member A2 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SLC8A2 transcript	NM_015063.3:c.2110+2073G>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	C=	A	G	T
GRCh38.p14 chr 19	NC_000019.10:g.47435389=	NC_000019.10:g.47435389C>A	NC_000019.10:g.47435389C>G	NC_000019.10:g.47435389C>T
GRCh37.p13 chr 19	NC_000019.9:g.47938646=	NC_000019.9:g.47938646C>A	NC_000019.9:g.47938646C>G	NC_000019.9:g.47938646C>T
SLC8A2 transcript	NM_015063.2:c.2110+2073=	NM_015063.2:c.2110+2073G>T	NM_015063.2:c.2110+2073G>C	NM_015063.2:c.2110+2073G>A
SLC8A2 transcript	NM_015063.3:c.2110+2073=	NM_015063.3:c.2110+2073G>T	NM_015063.3:c.2110+2073G>C	NM_015063.3:c.2110+2073G>A
SLC8A2 transcript variant X1	XM_005259172.1:c.2092+2073=	XM_005259172.1:c.2092+2073G>T	XM_005259172.1:c.2092+2073G>C	XM_005259172.1:c.2092+2073G>A

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#.

85 SubSNP, 17 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	KWOK	ss1135610	Oct 05, 2000 (86)
2	BCM_SSAHASNP	ss10939064	Jul 11, 2003 (116)
3	WI_SSAHASNP	ss12468866	Jul 11, 2003 (116)
4	SSAHASNP	ss21534868	Apr 05, 2004 (121)
5	BCMHGSC_JDW	ss90991171	Mar 24, 2008 (129)
6	HUMANGENOME_JCVI	ss96270556	Feb 06, 2009 (130)
7	BGI	ss106057777	Feb 06, 2009 (130)
8	1000GENOMES	ss115208636	Jan 25, 2009 (130)
9	ILLUMINA-UK	ss117722018	Feb 14, 2009 (130)
10	ENSEMBL	ss136252267	Dec 01, 2009 (131)
11	ENSEMBL	ss137703410	Dec 01, 2009 (131)
12	GMI	ss155955939	Dec 01, 2009 (131)
13	COMPLETE_GENOMICS	ss168273116	Jul 04, 2010 (132)
14	COMPLETE_GENOMICS	ss169895986	Jul 04, 2010 (132)
15	COMPLETE_GENOMICS	ss171802091	Jul 04, 2010 (132)
16	BUSHMAN	ss203771069	Jul 04, 2010 (132)
17	BCM-HGSC-SUB	ss208430204	Jul 04, 2010 (132)
18	1000GENOMES	ss210948235	Jul 14, 2010 (132)
19	1000GENOMES	ss228164320	Jul 14, 2010 (132)
20	1000GENOMES	ss237695281	Jul 15, 2010 (132)
21	1000GENOMES	ss243897020	Jul 15, 2010 (132)
22	BL	ss255714788	May 09, 2011 (134)
23	GMI	ss283230583	May 04, 2012 (137)
24	GMI	ss287391019	Apr 25, 2013 (138)
25	PJP	ss292186766	May 09, 2011 (134)
26	ILLUMINA	ss483411380	May 04, 2012 (137)
27	ILLUMINA	ss483837968	May 04, 2012 (137)
28	ILLUMINA	ss535622894	Sep 08, 2015 (146)
29	TISHKOFF	ss566019070	Apr 25, 2013 (138)
30	SSMP	ss661885753	Apr 25, 2013 (138)
31	ILLUMINA	ss780267300	Sep 08, 2015 (146)
32	ILLUMINA	ss782148905	Sep 08, 2015 (146)
33	ILLUMINA	ss835753289	Sep 08, 2015 (146)
34	JMKIDD_LAB	ss1081942956	Aug 21, 2014 (142)
35	1000GENOMES	ss1363403025	Aug 21, 2014 (142)
36	DDI	ss1428418785	Apr 01, 2015 (144)
37	EVA_GENOME_DK	ss1578660719	Apr 01, 2015 (144)
38	EVA_UK10K_ALSPAC	ss1638079510	Apr 01, 2015 (144)
39	EVA_UK10K_TWINSUK	ss1681073543	Apr 01, 2015 (144)
40	EVA_DECODE	ss1698413405	Apr 01, 2015 (144)
41	HAMMER_LAB	ss1809334159	Sep 08, 2015 (146)
42	WEILL_CORNELL_DGM	ss1937856256	Feb 12, 2016 (147)
43	GENOMED	ss1968653629	Jul 19, 2016 (147)
44	JJLAB	ss2029704390	Sep 14, 2016 (149)
45	USC_VALOUEV	ss2158249880	Dec 20, 2016 (150)
46	HUMAN_LONGEVITY	ss2226169664	Dec 20, 2016 (150)
47	SYSTEMSBIOZJU	ss2629349327	Nov 08, 2017 (151)
48	ILLUMINA	ss2633546465	Nov 08, 2017 (151)
49	GRF	ss2702862875	Nov 08, 2017 (151)
50	GNOMAD	ss2963557879	Nov 08, 2017 (151)
51	SWEGEN	ss3017574448	Nov 08, 2017 (151)
52	BIOINF_KMB_FNS_UNIBA	ss3028682446	Nov 08, 2017 (151)
53	CSHL	ss3352329478	Nov 08, 2017 (151)
54	ILLUMINA	ss3627946111	Oct 12, 2018 (152)
55	ILLUMINA	ss3631517266	Oct 12, 2018 (152)
56	ILLUMINA	ss3642063278	Oct 12, 2018 (152)
57	URBANLAB	ss3650928839	Oct 12, 2018 (152)
58	EVA_DECODE	ss3702885811	Jul 13, 2019 (153)
59	ACPOP	ss3743089555	Jul 13, 2019 (153)
60	EVA	ss3756133907	Jul 13, 2019 (153)
61	PACBIO	ss3788547092	Jul 13, 2019 (153)
62	PACBIO	ss3793454269	Jul 13, 2019 (153)
63	PACBIO	ss3798341159	Jul 13, 2019 (153)
64	KHV_HUMAN_GENOMES	ss3821381836	Jul 13, 2019 (153)
65	EVA	ss3835491107	Apr 27, 2020 (154)
66	EVA	ss3841368214	Apr 27, 2020 (154)
67	EVA	ss3846874419	Apr 27, 2020 (154)
68	SGDP_PRJ	ss3888346428	Apr 27, 2020 (154)
69	KRGDB	ss3938484427	Apr 27, 2020 (154)
70	KOGIC	ss3981484100	Apr 27, 2020 (154)
71	TOPMED	ss5076822133	Apr 26, 2021 (155)
72	TOMMO_GENOMICS	ss5228046210	Apr 26, 2021 (155)
73	1000G_HIGH_COVERAGE	ss5307468812	Oct 13, 2022 (156)
74	EVA	ss5315978617	Oct 13, 2022 (156)
75	EVA	ss5435210371	Oct 13, 2022 (156)
76	HUGCELL_USP	ss5499954407	Oct 13, 2022 (156)
77	1000G_HIGH_COVERAGE	ss5613294143	Oct 13, 2022 (156)
78	SANFORD_IMAGENETICS	ss5662513706	Oct 13, 2022 (156)
79	TOMMO_GENOMICS	ss5786775265	Oct 13, 2022 (156)
80	YY_MCH	ss5817653657	Oct 13, 2022 (156)
81	EVA	ss5840633580	Oct 13, 2022 (156)
82	EVA	ss5852311479	Oct 13, 2022 (156)
83	EVA	ss5928333302	Oct 13, 2022 (156)
84	EVA	ss5953922882	Oct 13, 2022 (156)
85	EVA	ss5981059453	Oct 13, 2022 (156)
86	1000Genomes	NC_000019.9 - 47938646	Oct 12, 2018 (152)
87	1000Genomes_30x	NC_000019.10 - 47435389	Oct 13, 2022 (156)
88	The Avon Longitudinal Study of Parents and Children	NC_000019.9 - 47938646	Oct 12, 2018 (152)
89	The Danish reference pan genome	NC_000019.9 - 47938646	Apr 27, 2020 (154)
90	gnomAD - Genomes	NC_000019.10 - 47435389	Apr 26, 2021 (155)
91	KOREAN population from KRGDB	NC_000019.9 - 47938646	Apr 27, 2020 (154)
92	Korean Genome Project	NC_000019.10 - 47435389	Apr 27, 2020 (154)
93	Northern Sweden	NC_000019.9 - 47938646	Jul 13, 2019 (153)
94	Qatari	NC_000019.9 - 47938646	Apr 27, 2020 (154)
95	SGDP_PRJ	NC_000019.9 - 47938646	Apr 27, 2020 (154)
96	Siberian	NC_000019.9 - 47938646	Apr 27, 2020 (154)
97	8.3KJPN	NC_000019.9 - 47938646	Apr 26, 2021 (155)
98	14KJPN	NC_000019.10 - 47435389	Oct 13, 2022 (156)
99	TopMed	NC_000019.10 - 47435389	Apr 26, 2021 (155)
100	UK 10K study - Twins	NC_000019.9 - 47938646	Oct 12, 2018 (152)
101	A Vietnamese Genetic Variation Database	NC_000019.9 - 47938646	Jul 13, 2019 (153)
102	ALFA	NC_000019.10 - 47435389	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
ss90991171, ss115208636, ss117722018, ss168273116, ss169895986, ss171802091, ss203771069, ss208430204, ss210948235, ss255714788, ss283230583, ss287391019, ss292186766, ss483837968, ss1698413405	NC_000019.8:52630457:C:A	NC_000019.10:47435388:C:A	(self)
76818476, 42534484, 4842441, 45661821, 16374420, 19898178, 40363408, 10766234, 86015517, 42534484, 9391120, ss228164320, ss237695281, ss243897020, ss483411380, ss535622894, ss566019070, ss661885753, ss780267300, ss782148905, ss835753289, ss1081942956, ss1363403025, ss1428418785, ss1578660719, ss1638079510, ss1681073543, ss1809334159, ss1937856256, ss1968653629, ss2029704390, ss2158249880, ss2629349327, ss2633546465, ss2702862875, ss2963557879, ss3017574448, ss3352329478, ss3627946111, ss3631517266, ss3642063278, ss3743089555, ss3756133907, ss3788547092, ss3793454269, ss3798341159, ss3835491107, ss3841368214, ss3888346428, ss3938484427, ss5228046210, ss5315978617, ss5435210371, ss5662513706, ss5840633580, ss5953922882, ss5981059453	NC_000019.9:47938645:C:A	NC_000019.10:47435388:C:A	(self)
100820078, 541765923, 37862101, 120612369, 292367797, 11633912981, ss2226169664, ss3028682446, ss3650928839, ss3702885811, ss3821381836, ss3846874419, ss3981484100, ss5076822133, ss5307468812, ss5499954407, ss5613294143, ss5786775265, ss5817653657, ss5852311479, ss5928333302	NC_000019.10:47435388:C:A	NC_000019.10:47435388:C:A	(self)
ss10939064, ss12468866, ss21534868	NT_011109.15:20206835:C:A	NC_000019.10:47435388:C:A	(self)
ss1135610, ss96270556, ss106057777, ss136252267, ss137703410, ss155955939	NT_011109.16:20206863:C:A	NC_000019.10:47435388:C:A	(self)
45661821, ss3938484427	NC_000019.9:47938645:C:G	NC_000019.10:47435388:C:G	(self)
45661821, ss3938484427	NC_000019.9:47938645:C:T	NC_000019.10:47435388: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 rs830154

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

rs830154