Name: rs75086406
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.

rs75086406

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:241513679 (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>G / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.000068 (18/264690, TOPMED)
T=0.000119 (30/251452, GnomAD_exome)
T=0.000123 (20/162166, ALFA) (+ 12 more)
T=0.000043 (6/140190, GnomAD)
T=0.000140 (17/121352, ExAC)
T=0.00020 (16/78700, PAGE_STUDY)
T=0.00046 (13/28256, 14KJPN)
T=0.00060 (10/16760, 8.3KJPN)
T=0.0003 (2/6404, 1000G_30x)
T=0.0004 (2/5008, 1000G)
T=0.0027 (8/2922, KOREAN)
T=0.0016 (3/1832, Korea1K)
T=0.003 (2/792, PRJEB37584)
C=0.5 (1/2, SGDP_PRJ)
T=0.5 (1/2, SGDP_PRJ)

Clinical Significance: Reported in ClinVar
Gene : Consequence: FH : Missense Variant
Publications: 2 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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	HTRZ	HWEP
Total	Global	162288	C=0.999877	T=0.000123	0.999754	0.000246	0
European	Sub	140824	C=1.000000	T=0.000000	1.0	0.0	N/A
African	Sub	4306	C=0.9998	T=0.0002	0.999536	0.000464	0
African Others	Sub	168	C=1.000	T=0.000	1.0	0.0	N/A
African American	Sub	4138	C=0.9998	T=0.0002	0.999517	0.000483	0
Asian	Sub	6294	C=0.9976	T=0.0024	0.995234	0.004766	0
East Asian	Sub	4476	C=0.9973	T=0.0027	0.994638	0.005362	0
Other Asian	Sub	1818	C=0.9983	T=0.0017	0.9967	0.0033	0
Latin American 1	Sub	442	C=1.000	T=0.000	1.0	0.0	N/A
Latin American 2	Sub	950	C=1.000	T=0.000	1.0	0.0	N/A
South Asian	Sub	280	C=1.000	T=0.000	1.0	0.0	N/A
Other	Sub	9192	C=0.9996	T=0.0004	0.99913	0.00087	0

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=0.999932	T=0.000068
gnomAD - Exomes	Global	Study-wide	251452	C=0.999881	T=0.000119
gnomAD - Exomes	European	Sub	135384	C=1.000000	T=0.000000
gnomAD - Exomes	Asian	Sub	49006	C=0.99943	T=0.00057
gnomAD - Exomes	American	Sub	34590	C=1.00000	T=0.00000
gnomAD - Exomes	African	Sub	16254	C=0.99988	T=0.00012
gnomAD - Exomes	Ashkenazi Jewish	Sub	10080	C=1.00000	T=0.00000
gnomAD - Exomes	Other	Sub	6138	C=1.0000	T=0.0000
Allele Frequency Aggregator	Total	Global	162166	C=0.999877	T=0.000123
Allele Frequency Aggregator	European	Sub	140720	C=1.000000	T=0.000000
Allele Frequency Aggregator	Other	Sub	9188	C=0.9996	T=0.0004
Allele Frequency Aggregator	Asian	Sub	6294	C=0.9976	T=0.0024
Allele Frequency Aggregator	African	Sub	4292	C=0.9998	T=0.0002
Allele Frequency Aggregator	Latin American 2	Sub	950	C=1.000	T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	442	C=1.000	T=0.000
Allele Frequency Aggregator	South Asian	Sub	280	C=1.000	T=0.000
gnomAD - Genomes	Global	Study-wide	140190	C=0.999957	T=0.000043
gnomAD - Genomes	European	Sub	75904	C=1.00000	T=0.00000
gnomAD - Genomes	African	Sub	42030	C=0.99995	T=0.00005
gnomAD - Genomes	American	Sub	13646	C=1.00000	T=0.00000
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	C=1.0000	T=0.0000
gnomAD - Genomes	East Asian	Sub	3134	C=0.9990	T=0.0010
gnomAD - Genomes	Other	Sub	2152	C=0.9995	T=0.0005
ExAC	Global	Study-wide	121352	C=0.999860	T=0.000140
ExAC	Europe	Sub	73328	C=1.00000	T=0.00000
ExAC	Asian	Sub	25156	C=0.99936	T=0.00064
ExAC	American	Sub	11570	C=1.00000	T=0.00000
ExAC	African	Sub	10390	C=0.99990	T=0.00010
ExAC	Other	Sub	908	C=1.000	T=0.000
The PAGE Study	Global	Study-wide	78700	C=0.99980	T=0.00020
The PAGE Study	AfricanAmerican	Sub	32514	C=0.99997	T=0.00003
The PAGE Study	Mexican	Sub	10810	C=0.99991	T=0.00009
The PAGE Study	Asian	Sub	8318	C=0.9990	T=0.0010
The PAGE Study	PuertoRican	Sub	7918	C=0.9999	T=0.0001
The PAGE Study	NativeHawaiian	Sub	4534	C=0.9996	T=0.0004
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=1.0000	T=0.0000
The PAGE Study	SouthAsian	Sub	856	C=0.996	T=0.004
14KJPN	JAPANESE	Study-wide	28256	C=0.99954	T=0.00046
8.3KJPN	JAPANESE	Study-wide	16760	C=0.99940	T=0.00060
1000Genomes_30x	Global	Study-wide	6404	C=0.9997	T=0.0003
1000Genomes_30x	African	Sub	1786	C=1.0000	T=0.0000
1000Genomes_30x	Europe	Sub	1266	C=1.0000	T=0.0000
1000Genomes_30x	South Asian	Sub	1202	C=0.9992	T=0.0008
1000Genomes_30x	East Asian	Sub	1170	C=0.9991	T=0.0009
1000Genomes_30x	American	Sub	980	C=1.000	T=0.000
1000Genomes	Global	Study-wide	5008	C=0.9996	T=0.0004
1000Genomes	African	Sub	1322	C=1.0000	T=0.0000
1000Genomes	East Asian	Sub	1008	C=0.9990	T=0.0010
1000Genomes	Europe	Sub	1006	C=1.0000	T=0.0000
1000Genomes	South Asian	Sub	978	C=0.999	T=0.001
1000Genomes	American	Sub	694	C=1.000	T=0.000
KOREAN population from KRGDB	KOREAN	Study-wide	2922	C=0.9973	T=0.0027
Korean Genome Project	KOREAN	Study-wide	1832	C=0.9984	T=0.0016
CNV burdens in cranial meningiomas	Global	Study-wide	792	C=0.997	T=0.003
CNV burdens in cranial meningiomas	CRM	Sub	792	C=0.997	T=0.003
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 1	NC_000001.11:g.241513679C>G
GRCh38.p14 chr 1	NC_000001.11:g.241513679C>T
GRCh37.p13 chr 1	NC_000001.10:g.241676979C>G
GRCh37.p13 chr 1	NC_000001.10:g.241676979C>T
FH RefSeqGene (LRG_504)	NG_012338.1:g.11076G>C
FH RefSeqGene (LRG_504)	NG_012338.1:g.11076G>A

Gene: FH, fumarate hydratase (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
FH transcript	NM_000143.4:c.302G>C	R [CGA] > P [CCA]	Coding Sequence Variant
fumarate hydratase, mitochondrial	NP_000134.2:p.Arg101Pro	R (Arg) > P (Pro)	Missense Variant
FH transcript	NM_000143.4:c.302G>A	R [CGA] > Q [CAA]	Coding Sequence Variant
fumarate hydratase, mitochondrial	NP_000134.2:p.Arg101Gln	R (Arg) > Q (Gln)	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: G (allele ID: 31277 )

ClinVar Accession	Disease Names	Clinical Significance
RCV000017625.29	Hereditary leiomyomatosis and renal cell cancer	Pathogenic
RCV000489422.2	not provided	Likely-Pathogenic

Allele: T (allele ID: 391111 )

ClinVar Accession	Disease Names	Clinical Significance
RCV000466487.8	Fumarase deficiency	Uncertain-Significance
RCV001018184.1	Hereditary cancer-predisposing syndrome	Uncertain-Significance
RCV001546164.3	not provided	Uncertain-Significance

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=	G	T
GRCh38.p14 chr 1	NC_000001.11:g.241513679=	NC_000001.11:g.241513679C>G	NC_000001.11:g.241513679C>T
GRCh37.p13 chr 1	NC_000001.10:g.241676979=	NC_000001.10:g.241676979C>G	NC_000001.10:g.241676979C>T
FH RefSeqGene (LRG_504)	NG_012338.1:g.11076=	NG_012338.1:g.11076G>C	NG_012338.1:g.11076G>A
FH transcript	NM_000143.4:c.302=	NM_000143.4:c.302G>C	NM_000143.4:c.302G>A
FH transcript	NM_000143.3:c.302=	NM_000143.3:c.302G>C	NM_000143.3:c.302G>A
fumarate hydratase, mitochondrial	NP_000134.2:p.Arg101=	NP_000134.2:p.Arg101Pro	NP_000134.2:p.Arg101Gln

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#.

48 SubSNP, 14 Frequency, 5 ClinVar submissions

No	Submitter	Submission ID	Date (Build)
1	ILLUMINA	ss161046557	Dec 01, 2009 (131)
2	OMIM-CURATED-RECORDS	ss275514591	Nov 22, 2010 (133)
3	1000GENOMES	ss454780449	Sep 17, 2011 (135)
4	ILLUMINA	ss479315574	Sep 08, 2015 (146)
5	1000GENOMES	ss489799262	May 04, 2012 (137)
6	EXOME_CHIP	ss491313316	May 04, 2012 (137)
7	ILLUMINA	ss780802871	Sep 08, 2015 (146)
8	ILLUMINA	ss783484352	Sep 08, 2015 (146)
9	1000GENOMES	ss1295352401	Aug 21, 2014 (142)
10	EVA_EXAC	ss1686137724	Apr 01, 2015 (144)
11	ILLUMINA	ss1751909294	Sep 08, 2015 (146)
12	ILLUMINA	ss1917744623	Feb 12, 2016 (147)
13	ILLUMINA	ss1946028671	Feb 12, 2016 (147)
14	ILLUMINA	ss1958374004	Feb 12, 2016 (147)
15	GNOMAD	ss2732402686	Nov 08, 2017 (151)
16	GNOMAD	ss2746600887	Nov 08, 2017 (151)
17	GNOMAD	ss2768185054	Nov 08, 2017 (151)
18	ILLUMINA	ss3021198624	Nov 08, 2017 (151)
19	ILLUMINA	ss3626351164	Oct 11, 2018 (152)
20	ILLUMINA	ss3634382524	Oct 11, 2018 (152)
21	ILLUMINA	ss3636061841	Oct 11, 2018 (152)
22	ILLUMINA	ss3640089877	Oct 11, 2018 (152)
23	ILLUMINA	ss3644524680	Oct 11, 2018 (152)
24	ILLUMINA	ss3651544773	Oct 11, 2018 (152)
25	ILLUMINA	ss3725122196	Jul 12, 2019 (153)
26	ILLUMINA	ss3744362492	Jul 12, 2019 (153)
27	ILLUMINA	ss3744683422	Jul 12, 2019 (153)
28	EVA	ss3747558345	Jul 12, 2019 (153)
29	PAGE_CC	ss3770885211	Jul 12, 2019 (153)
30	ILLUMINA	ss3772184190	Jul 12, 2019 (153)
31	KHV_HUMAN_GENOMES	ss3800561974	Jul 12, 2019 (153)
32	SGDP_PRJ	ss3851270333	Apr 25, 2020 (154)
33	KRGDB	ss3896630774	Apr 25, 2020 (154)
34	KOGIC	ss3946853243	Apr 25, 2020 (154)
35	EVA	ss3984475180	Apr 25, 2021 (155)
36	TOPMED	ss4489623115	Apr 25, 2021 (155)
37	TOMMO_GENOMICS	ss5149234480	Apr 25, 2021 (155)
38	EVA	ss5237285374	Apr 25, 2021 (155)
39	1000G_HIGH_COVERAGE	ss5246413122	Oct 17, 2022 (156)
40	EVA	ss5314697853	Oct 17, 2022 (156)
41	EVA	ss5325911557	Oct 17, 2022 (156)
42	1000G_HIGH_COVERAGE	ss5520816736	Oct 17, 2022 (156)
43	TOMMO_GENOMICS	ss5677226572	Oct 17, 2022 (156)
44	YY_MCH	ss5801798956	Oct 17, 2022 (156)
45	EVA	ss5847581270	Oct 17, 2022 (156)
46	EVA	ss5912682693	Oct 17, 2022 (156)
47	EVA	ss5935545839	Oct 17, 2022 (156)
48	EVA	ss5939652110	Oct 17, 2022 (156)
49	1000Genomes	NC_000001.10 - 241676979	Oct 11, 2018 (152)
50	1000Genomes_30x	NC_000001.11 - 241513679	Oct 17, 2022 (156)
51	ExAC	NC_000001.10 - 241676979	Oct 11, 2018 (152)
52	gnomAD - Genomes	NC_000001.11 - 241513679	Apr 25, 2021 (155)
53	gnomAD - Exomes	NC_000001.10 - 241676979	Jul 12, 2019 (153)
54	KOREAN population from KRGDB	NC_000001.10 - 241676979	Apr 25, 2020 (154)
55	Korean Genome Project	NC_000001.11 - 241513679	Apr 25, 2020 (154)
56	The PAGE Study	NC_000001.11 - 241513679	Jul 12, 2019 (153)
57	CNV burdens in cranial meningiomas	NC_000001.10 - 241676979	Apr 25, 2021 (155)
58	SGDP_PRJ	NC_000001.10 - 241676979	Apr 25, 2020 (154)
59	8.3KJPN	NC_000001.10 - 241676979	Apr 25, 2021 (155)
60	14KJPN	NC_000001.11 - 241513679	Oct 17, 2022 (156)
61	TopMed	NC_000001.11 - 241513679	Apr 25, 2021 (155)
62	ALFA	NC_000001.11 - 241513679	Apr 25, 2021 (155)
63	ClinVar	RCV000017625.29	Oct 11, 2018 (152)
64	ClinVar	RCV000466487.8	Oct 17, 2022 (156)
65	ClinVar	RCV000489422.2	Oct 17, 2022 (156)
66	ClinVar	RCV001018184.1	Apr 25, 2020 (154)
67	ClinVar	RCV001546164.3	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
ss5847581270	NC_000001.10:241676978:C:G	NC_000001.11:241513678:C:G
RCV000017625.29, RCV000489422.2, ss275514591	NC_000001.11:241513678:C:G	NC_000001.11:241513678:C:G	(self)
6233320, 5380690, 1441659, 3808168, 24503, 3287313, 7203787, ss454780449, ss479315574, ss489799262, ss491313316, ss780802871, ss783484352, ss1295352401, ss1686137724, ss1751909294, ss1917744623, ss1946028671, ss1958374004, ss2732402686, ss2746600887, ss2768185054, ss3021198624, ss3626351164, ss3634382524, ss3636061841, ss3640089877, ss3644524680, ss3651544773, ss3744362492, ss3744683422, ss3747558345, ss3772184190, ss3851270333, ss3896630774, ss3984475180, ss5149234480, ss5237285374, ss5314697853, ss5325911557, ss5847581270, ss5935545839, ss5939652110	NC_000001.10:241676978:C:T	NC_000001.11:241513678:C:T	(self)
RCV000466487.8, RCV001018184.1, RCV001546164.3, 8342671, 44590145, 3231244, 106680, 11063676, 53229450, 10695595350, ss3725122196, ss3770885211, ss3800561974, ss3946853243, ss4489623115, ss5246413122, ss5520816736, ss5677226572, ss5801798956, ss5912682693	NC_000001.11:241513678:C:T	NC_000001.11:241513678:C:T	(self)
ss161046557	NT_167186.1:35194757:C:T	NC_000001.11:241513678:C:T	(self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

2 citations for rs75086406

PMID	Title	Author	Year	Journal
15663510	Familial multiple cutaneous and uterine leiomyomas associated with papillary renal cell cancer.	Chan I et al.	2005	Clinical and experimental dermatology
17908262	Evidence for a founder effect of the germline fumarate hydratase gene mutation R58P causing hereditary leiomyomatosis and renal cell cancer (HLRCC).	Heinritz W et al.	2008	Annals of human genetics

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

rs75086406