Name: rs147398624
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.

rs147398624

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:148120221 (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>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.000397 (105/264690, TOPMED)
T=0.000450 (113/250842, GnomAD_exome)
T=0.000527 (105/199270, ALFA) (+ 11 more)
T=0.000435 (61/140232, GnomAD)
T=0.000504 (61/121060, ExAC)
T=0.00025 (20/78702, PAGE_STUDY)
T=0.00054 (7/13006, GO-ESP)
T=0.0009 (6/6404, 1000G_30x)
T=0.0010 (5/5008, 1000G)
T=0.0008 (3/3854, ALSPAC)
T=0.0008 (3/3708, TWINSUK)
T=0.001 (1/792, PRJEB37584)
C=0.5 (1/2, SGDP_PRJ)
T=0.5 (1/2, SGDP_PRJ)

Clinical Significance: Reported in ClinVar
Gene : Consequence: NR3C2 : Missense 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	215682	C=0.999453	T=0.000547
European	Sub	180070	C=0.999389	T=0.000611
African	Sub	9792	C=0.9999	T=0.0001
African Others	Sub	360	C=1.000	T=0.000
African American	Sub	9432	C=0.9999	T=0.0001
Asian	Sub	6350	C=0.9998	T=0.0002
East Asian	Sub	4502	C=1.0000	T=0.0000
Other Asian	Sub	1848	C=0.9995	T=0.0005
Latin American 1	Sub	796	C=0.999	T=0.001
Latin American 2	Sub	968	C=1.000	T=0.000
South Asian	Sub	280	C=1.000	T=0.000
Other	Sub	17426	C=0.99971	T=0.00029

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=0.999603	T=0.000397
gnomAD - Exomes	Global	Study-wide	250842	C=0.999550	T=0.000450
gnomAD - Exomes	European	Sub	134848	C=0.999503	T=0.000497
gnomAD - Exomes	Asian	Sub	49002	C=0.99927	T=0.00073
gnomAD - Exomes	American	Sub	34578	C=0.99994	T=0.00006
gnomAD - Exomes	African	Sub	16236	C=0.99975	T=0.00025
gnomAD - Exomes	Ashkenazi Jewish	Sub	10060	C=1.00000	T=0.00000
gnomAD - Exomes	Other	Sub	6118	C=0.9993	T=0.0007
Allele Frequency Aggregator	Total	Global	199270	C=0.999473	T=0.000527
Allele Frequency Aggregator	European	Sub	169930	C=0.999423	T=0.000577
Allele Frequency Aggregator	Other	Sub	15992	C=0.99969	T=0.00031
Allele Frequency Aggregator	Asian	Sub	6350	C=0.9998	T=0.0002
Allele Frequency Aggregator	African	Sub	4954	C=1.0000	T=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	968	C=1.000	T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	796	C=0.999	T=0.001
Allele Frequency Aggregator	South Asian	Sub	280	C=1.000	T=0.000
gnomAD - Genomes	Global	Study-wide	140232	C=0.999565	T=0.000435
gnomAD - Genomes	European	Sub	75948	C=0.99945	T=0.00055
gnomAD - Genomes	African	Sub	42020	C=0.99981	T=0.00019
gnomAD - Genomes	American	Sub	13656	C=0.99985	T=0.00015
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	C=1.0000	T=0.0000
gnomAD - Genomes	East Asian	Sub	3134	C=0.9978	T=0.0022
gnomAD - Genomes	Other	Sub	2150	C=0.9991	T=0.0009
ExAC	Global	Study-wide	121060	C=0.999496	T=0.000504
ExAC	Europe	Sub	73182	C=0.99944	T=0.00056
ExAC	Asian	Sub	25114	C=0.99940	T=0.00060
ExAC	American	Sub	11538	C=0.99991	T=0.00009
ExAC	African	Sub	10322	C=0.99971	T=0.00029
ExAC	Other	Sub	904	C=0.999	T=0.001
The PAGE Study	Global	Study-wide	78702	C=0.99975	T=0.00025
The PAGE Study	AfricanAmerican	Sub	32516	C=0.99969	T=0.00031
The PAGE Study	Mexican	Sub	10810	C=0.99991	T=0.00009
The PAGE Study	Asian	Sub	8318	C=0.9998	T=0.0002
The PAGE Study	PuertoRican	Sub	7918	C=0.9997	T=0.0003
The PAGE Study	NativeHawaiian	Sub	4534	C=0.9991	T=0.0009
The PAGE Study	Cuban	Sub	4230	C=1.0000	T=0.0000
The PAGE Study	Dominican	Sub	3828	C=1.0000	T=0.0000
The PAGE Study	CentralAmerican	Sub	2450	C=1.0000	T=0.0000
The PAGE Study	SouthAmerican	Sub	1982	C=1.0000	T=0.0000
The PAGE Study	NativeAmerican	Sub	1260	C=0.9992	T=0.0008
The PAGE Study	SouthAsian	Sub	856	C=1.000	T=0.000
GO Exome Sequencing Project	Global	Study-wide	13006	C=0.99946	T=0.00054
GO Exome Sequencing Project	European American	Sub	8600	C=0.9993	T=0.0007
GO Exome Sequencing Project	African American	Sub	4406	C=0.9998	T=0.0002
1000Genomes_30x	Global	Study-wide	6404	C=0.9991	T=0.0009
1000Genomes_30x	African	Sub	1786	C=1.0000	T=0.0000
1000Genomes_30x	Europe	Sub	1266	C=0.9992	T=0.0008
1000Genomes_30x	South Asian	Sub	1202	C=1.0000	T=0.0000
1000Genomes_30x	East Asian	Sub	1170	C=0.9957	T=0.0043
1000Genomes_30x	American	Sub	980	C=1.000	T=0.000
1000Genomes	Global	Study-wide	5008	C=0.9990	T=0.0010
1000Genomes	African	Sub	1322	C=1.0000	T=0.0000
1000Genomes	East Asian	Sub	1008	C=0.9960	T=0.0040
1000Genomes	Europe	Sub	1006	C=0.9990	T=0.0010
1000Genomes	South Asian	Sub	978	C=1.000	T=0.000
1000Genomes	American	Sub	694	C=1.000	T=0.000
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.9992	T=0.0008
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.9992	T=0.0008
CNV burdens in cranial meningiomas	Global	Study-wide	792	C=0.999	T=0.001
CNV burdens in cranial meningiomas	CRM	Sub	792	C=0.999	T=0.001
SGDP_PRJ	Global	Study-wide	2	C=0.5	T=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 4	NC_000004.12:g.148120221C>T
GRCh37.p13 chr 4	NC_000004.11:g.149041372C>T
NR3C2 RefSeqGene	NG_013350.2:g.330287G>A
NR3C2 RefSeqGene	NG_013350.1:g.327301G>A

Gene: NR3C2, nuclear receptor subfamily 3 group C member 2 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
NR3C2 transcript variant 3	NM_001354819.1:c.2227G>A	V [GTT] > I [ATT]	Coding Sequence Variant
mineralocorticoid receptor isoform 2	NP_001341748.1:p.Val743Ile	V (Val) > I (Ile)	Missense Variant
NR3C2 transcript variant 1	NM_000901.5:c.2578G>A	V [GTT] > I [ATT]	Coding Sequence Variant
mineralocorticoid receptor isoform 1	NP_000892.2:p.Val860Ile	V (Val) > I (Ile)	Missense Variant
NR3C2 transcript variant 2	NM_001166104.2:c.2227G>A	V [GTT] > I [ATT]	Coding Sequence Variant
mineralocorticoid receptor isoform 2	NP_001159576.1:p.Val743Ile	V (Val) > I (Ile)	Missense Variant
NR3C2 transcript variant 4	NR_148974.2:n.2339G>A	N/A	Non Coding Transcript Variant
NR3C2 transcript variant X5	XM_011531978.3:c.	N/A	Genic Downstream Transcript Variant
NR3C2 transcript variant X6	XM_047415709.1:c.	N/A	Genic Downstream Transcript Variant
NR3C2 transcript variant X1	XM_011531975.2:c.2590G>A	V [GTT] > I [ATT]	Coding Sequence Variant
mineralocorticoid receptor isoform X1	XP_011530277.1:p.Val864Ile	V (Val) > I (Ile)	Missense Variant
NR3C2 transcript variant X2	XM_047415706.1:c.2578G>A	V [GTT] > I [ATT]	Coding Sequence Variant
mineralocorticoid receptor isoform X2	XP_047271662.1:p.Val860Ile	V (Val) > I (Ile)	Missense Variant
NR3C2 transcript variant X3	XM_047415707.1:c.2578G>A	V [GTT] > I [ATT]	Coding Sequence Variant
mineralocorticoid receptor isoform X2	XP_047271663.1:p.Val860Ile	V (Val) > I (Ile)	Missense Variant
NR3C2 transcript variant X4	XM_047415708.1:c.2578G>A	V [GTT] > I [ATT]	Coding Sequence Variant
mineralocorticoid receptor isoform X2	XP_047271664.1:p.Val860Ile	V (Val) > I (Ile)	Missense 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: T (allele ID: 292444 )

ClinVar Accession	Disease Names	Clinical Significance
RCV000364190.3	Autosomal dominant pseudohypoaldosteronism type 1	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	C=	T
GRCh38.p14 chr 4	NC_000004.12:g.148120221=	NC_000004.12:g.148120221C>T
GRCh37.p13 chr 4	NC_000004.11:g.149041372=	NC_000004.11:g.149041372C>T
NR3C2 RefSeqGene	NG_013350.2:g.330287=	NG_013350.2:g.330287G>A
NR3C2 RefSeqGene	NG_013350.1:g.327301=	NG_013350.1:g.327301G>A
NR3C2 transcript variant 1	NM_000901.5:c.2578=	NM_000901.5:c.2578G>A
NR3C2 transcript variant 1	NM_000901.4:c.2578=	NM_000901.4:c.2578G>A
NR3C2 transcript variant 4	NR_148974.2:n.2339=	NR_148974.2:n.2339G>A
NR3C2 transcript variant 4	NR_148974.1:n.2445=	NR_148974.1:n.2445G>A
NR3C2 transcript variant 2	NM_001166104.2:c.2227=	NM_001166104.2:c.2227G>A
NR3C2 transcript variant 2	NM_001166104.1:c.2227=	NM_001166104.1:c.2227G>A
NR3C2 transcript variant 3	NM_001354819.1:c.2227=	NM_001354819.1:c.2227G>A
NR3C2 transcript variant X1	XM_011531975.2:c.2590=	XM_011531975.2:c.2590G>A
NR3C2 transcript variant X1	XM_011531975.1:c.2590=	XM_011531975.1:c.2590G>A
NR3C2 transcript variant X2	XM_047415706.1:c.2578=	XM_047415706.1:c.2578G>A
NR3C2 transcript variant X4	XM_047415708.1:c.2578=	XM_047415708.1:c.2578G>A
NR3C2 transcript variant X3	XM_047415707.1:c.2578=	XM_047415707.1:c.2578G>A
mineralocorticoid receptor isoform 1	NP_000892.2:p.Val860=	NP_000892.2:p.Val860Ile
mineralocorticoid receptor isoform 2	NP_001159576.1:p.Val743=	NP_001159576.1:p.Val743Ile
mineralocorticoid receptor isoform 2	NP_001341748.1:p.Val743=	NP_001341748.1:p.Val743Ile
mineralocorticoid receptor isoform X1	XP_011530277.1:p.Val864=	XP_011530277.1:p.Val864Ile
mineralocorticoid receptor isoform X2	XP_047271662.1:p.Val860=	XP_047271662.1:p.Val860Ile
mineralocorticoid receptor isoform X2	XP_047271664.1:p.Val860=	XP_047271664.1:p.Val860Ile
mineralocorticoid receptor isoform X2	XP_047271663.1:p.Val860=	XP_047271663.1:p.Val860Ile

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#.

50 SubSNP, 13 Frequency, 1 ClinVar submissions

No	Submitter	Submission ID	Date (Build)
1	1000GENOMES	ss332034199	May 09, 2011 (134)
2	NHLBI-ESP	ss342172564	May 09, 2011 (134)
3	1000GENOMES	ss490895571	May 04, 2012 (137)
4	EXOME_CHIP	ss491361294	May 04, 2012 (137)
5	SSMP	ss651754773	Apr 25, 2013 (138)
6	ILLUMINA	ss780833027	Sep 08, 2015 (146)
7	ILLUMINA	ss783516021	Sep 08, 2015 (146)
8	1000GENOMES	ss1312327864	Aug 21, 2014 (142)
9	EVA_DECODE	ss1590326063	Apr 01, 2015 (144)
10	EVA_UK10K_ALSPAC	ss1611439462	Apr 01, 2015 (144)
11	EVA_UK10K_TWINSUK	ss1654433495	Apr 01, 2015 (144)
12	EVA_EXAC	ss1687657894	Apr 01, 2015 (144)
13	ILLUMINA	ss1752502221	Sep 08, 2015 (146)
14	ILLUMINA	ss1917785264	Feb 12, 2016 (147)
15	ILLUMINA	ss1946129550	Feb 12, 2016 (147)
16	ILLUMINA	ss1958728588	Feb 12, 2016 (147)
17	HUMAN_LONGEVITY	ss2268185538	Dec 20, 2016 (150)
18	GNOMAD	ss2734767146	Nov 08, 2017 (151)
19	GNOMAD	ss2747312416	Nov 08, 2017 (151)
20	GNOMAD	ss2816735171	Nov 08, 2017 (151)
21	AFFY	ss2985305859	Nov 08, 2017 (151)
22	AFFY	ss2985933531	Nov 08, 2017 (151)
23	ILLUMINA	ss3022424899	Nov 08, 2017 (151)
24	ILLUMINA	ss3629089875	Oct 12, 2018 (152)
25	ILLUMINA	ss3634974846	Oct 12, 2018 (152)
26	ILLUMINA	ss3640682140	Oct 12, 2018 (152)
27	ILLUMINA	ss3644862387	Oct 12, 2018 (152)
28	ILLUMINA	ss3652915100	Oct 12, 2018 (152)
29	ILLUMINA	ss3654077836	Oct 12, 2018 (152)
30	EVA_DECODE	ss3713307322	Jul 13, 2019 (153)
31	ILLUMINA	ss3726179498	Jul 13, 2019 (153)
32	ILLUMINA	ss3744530464	Jul 13, 2019 (153)
33	ILLUMINA	ss3745275073	Jul 13, 2019 (153)
34	EVA	ss3762565972	Jul 13, 2019 (153)
35	PAGE_CC	ss3771160188	Jul 13, 2019 (153)
36	ILLUMINA	ss3772769521	Jul 13, 2019 (153)
37	KHV_HUMAN_GENOMES	ss3805727247	Jul 13, 2019 (153)
38	EVA	ss3824050313	Apr 26, 2020 (154)
39	EVA	ss3825665264	Apr 26, 2020 (154)
40	SGDP_PRJ	ss3860326630	Apr 26, 2020 (154)
41	EVA	ss3984536674	Apr 26, 2021 (155)
42	TOPMED	ss4636491877	Apr 26, 2021 (155)
43	1000G_HIGH_COVERAGE	ss5261471023	Oct 17, 2022 (156)
44	TRAN_CS_UWATERLOO	ss5314411589	Oct 17, 2022 (156)
45	EVA	ss5353115513	Oct 17, 2022 (156)
46	1000G_HIGH_COVERAGE	ss5543804838	Oct 17, 2022 (156)
47	EVA	ss5848028139	Oct 17, 2022 (156)
48	EVA	ss5854498628	Oct 17, 2022 (156)
49	EVA	ss5866013563	Oct 17, 2022 (156)
50	EVA	ss5964761064	Oct 17, 2022 (156)
51	1000Genomes	NC_000004.11 - 149041372	Oct 12, 2018 (152)
52	1000Genomes_30x	NC_000004.12 - 148120221	Oct 17, 2022 (156)
53	The Avon Longitudinal Study of Parents and Children	NC_000004.11 - 149041372	Oct 12, 2018 (152)
54	ExAC	NC_000004.11 - 149041372	Oct 12, 2018 (152)
55	gnomAD - Genomes	NC_000004.12 - 148120221	Apr 26, 2021 (155)
56	gnomAD - Exomes	NC_000004.11 - 149041372	Jul 13, 2019 (153)
57	GO Exome Sequencing Project	NC_000004.11 - 149041372	Oct 12, 2018 (152)
58	The PAGE Study	NC_000004.12 - 148120221	Jul 13, 2019 (153)
59	CNV burdens in cranial meningiomas	NC_000004.11 - 149041372	Apr 26, 2021 (155)
60	SGDP_PRJ	NC_000004.11 - 149041372	Apr 26, 2020 (154)
61	TopMed	NC_000004.12 - 148120221	Apr 26, 2021 (155)
62	UK 10K study - Twins	NC_000004.11 - 149041372	Oct 12, 2018 (152)
63	ALFA	NC_000004.12 - 148120221	Apr 26, 2021 (155)
64	ClinVar	RCV000364190.3	Oct 17, 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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss1590326063	NC_000004.10:149260821:C:T	NC_000004.12:148120220:C:T	(self)
23822366, 13245428, 7636498, 3878383, 508497, 86036, 12343610, 13245428, ss332034199, ss342172564, ss490895571, ss491361294, ss651754773, ss780833027, ss783516021, ss1312327864, ss1611439462, ss1654433495, ss1687657894, ss1752502221, ss1917785264, ss1946129550, ss1958728588, ss2734767146, ss2747312416, ss2816735171, ss2985305859, ss2985933531, ss3022424899, ss3629089875, ss3634974846, ss3640682140, ss3644862387, ss3652915100, ss3654077836, ss3744530464, ss3745275073, ss3762565972, ss3772769521, ss3824050313, ss3825665264, ss3860326630, ss3984536674, ss5353115513, ss5848028139, ss5964761064	NC_000004.11:149041371:C:T	NC_000004.12:148120220:C:T	(self)
RCV000364190.3, 31330773, 168734941, 381657, 473869433, 10898318582, ss2268185538, ss3713307322, ss3726179498, ss3771160188, ss3805727247, ss4636491877, ss5261471023, ss5314411589, ss5543804838, ss5854498628, ss5866013563	NC_000004.12:148120220:C:T	NC_000004.12:148120220: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 rs147398624

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

rs147398624