Name: rs11558855
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.

rs11558855

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr10:11742634 (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=0.136888 (36233/264690, TOPMED)
T=0.145359 (20307/139702, GnomAD)
T=0.02230 (630/28254, 14KJPN) (+ 18 more)
T=0.16984 (3208/18888, ALFA)
T=0.02292 (384/16756, 8.3KJPN)
T=0.1055 (979/9280, GO-ESP)
T=0.1559 (1032/6620, GnomAD_exome)
T=0.0921 (590/6404, 1000G_30x)
T=0.0919 (460/5008, 1000G)
T=0.1897 (850/4480, Estonian)
T=0.2138 (824/3854, ALSPAC)
T=0.2101 (779/3708, TWINSUK)
T=0.0050 (14/2828, KOREAN)
T=0.0045 (8/1770, Korea1K)
T=0.215 (129/600, NorthernSweden)
T=0.372 (148/398, ExAC)
T=0.120 (26/216, Qatari)
C=0.48 (47/98, SGDP_PRJ)
T=0.17 (7/40, GENOME_DK)
C=0.5 (5/10, Siberian)
T=0.5 (5/10, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ECHDC3 : 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	18888	C=0.83016	T=0.16984
European	Sub	14284	C=0.80321	T=0.19679
African	Sub	2946	C=0.9321	T=0.0679
African Others	Sub	114	C=0.965	T=0.035
African American	Sub	2832	C=0.9308	T=0.0692
Asian	Sub	112	C=0.991	T=0.009
East Asian	Sub	86	C=0.99	T=0.01
Other Asian	Sub	26	C=1.00	T=0.00
Latin American 1	Sub	146	C=0.877	T=0.123
Latin American 2	Sub	610	C=0.900	T=0.100
South Asian	Sub	98	C=0.83	T=0.17
Other	Sub	692	C=0.855	T=0.145

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=0.863112	T=0.136888
gnomAD - Genomes	Global	Study-wide	139702	C=0.854641	T=0.145359
gnomAD - Genomes	European	Sub	75586	C=0.80680	T=0.19320
gnomAD - Genomes	African	Sub	41920	C=0.92827	T=0.07173
gnomAD - Genomes	American	Sub	13608	C=0.87169	T=0.12831
gnomAD - Genomes	Ashkenazi Jewish	Sub	3318	C=0.8035	T=0.1965
gnomAD - Genomes	East Asian	Sub	3130	C=0.9907	T=0.0093
gnomAD - Genomes	Other	Sub	2140	C=0.8738	T=0.1262
14KJPN	JAPANESE	Study-wide	28254	C=0.97770	T=0.02230
Allele Frequency Aggregator	Total	Global	18888	C=0.83016	T=0.16984
Allele Frequency Aggregator	European	Sub	14284	C=0.80321	T=0.19679
Allele Frequency Aggregator	African	Sub	2946	C=0.9321	T=0.0679
Allele Frequency Aggregator	Other	Sub	692	C=0.855	T=0.145
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.900	T=0.100
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.877	T=0.123
Allele Frequency Aggregator	Asian	Sub	112	C=0.991	T=0.009
Allele Frequency Aggregator	South Asian	Sub	98	C=0.83	T=0.17
8.3KJPN	JAPANESE	Study-wide	16756	C=0.97708	T=0.02292
GO Exome Sequencing Project	Global	Study-wide	9280	C=0.8945	T=0.1055
GO Exome Sequencing Project	European American	Sub	6256	C=0.8660	T=0.1340
GO Exome Sequencing Project	African American	Sub	3024	C=0.9534	T=0.0466
gnomAD - Exomes	Global	Study-wide	6620	C=0.8441	T=0.1559
gnomAD - Exomes	European	Sub	3204	C=0.8146	T=0.1854
gnomAD - Exomes	Asian	Sub	1494	C=0.8668	T=0.1332
gnomAD - Exomes	American	Sub	960	C=0.901	T=0.099
gnomAD - Exomes	Ashkenazi Jewish	Sub	608	C=0.834	T=0.166
gnomAD - Exomes	Other	Sub	208	C=0.846	T=0.154
gnomAD - Exomes	African	Sub	146	C=0.925	T=0.075
1000Genomes_30x	Global	Study-wide	6404	C=0.9079	T=0.0921
1000Genomes_30x	African	Sub	1786	C=0.9574	T=0.0426
1000Genomes_30x	Europe	Sub	1266	C=0.8286	T=0.1714
1000Genomes_30x	South Asian	Sub	1202	C=0.8669	T=0.1331
1000Genomes_30x	East Asian	Sub	1170	C=0.9880	T=0.0120
1000Genomes_30x	American	Sub	980	C=0.874	T=0.126
1000Genomes	Global	Study-wide	5008	C=0.9081	T=0.0919
1000Genomes	African	Sub	1322	C=0.9576	T=0.0424
1000Genomes	East Asian	Sub	1008	C=0.9831	T=0.0169
1000Genomes	Europe	Sub	1006	C=0.8300	T=0.1700
1000Genomes	South Asian	Sub	978	C=0.868	T=0.132
1000Genomes	American	Sub	694	C=0.875	T=0.125
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.8103	T=0.1897
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.7862	T=0.2138
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.7899	T=0.2101
KOREAN population from KRGDB	KOREAN	Study-wide	2828	C=0.9950	T=0.0050
Korean Genome Project	KOREAN	Study-wide	1770	C=0.9955	T=0.0045
Northern Sweden	ACPOP	Study-wide	600	C=0.785	T=0.215
ExAC	Global	Study-wide	398	C=0.628	T=0.372
ExAC	Asian	Sub	236	C=0.627	T=0.373
ExAC	Europe	Sub	134	C=0.619	T=0.381
ExAC	African	Sub	12	C=0.67	T=0.33
ExAC	American	Sub	8	C=0.8	T=0.2
ExAC	Other	Sub	8	C=0.6	T=0.4
Qatari	Global	Study-wide	216	C=0.880	T=0.120
SGDP_PRJ	Global	Study-wide	98	C=0.48	T=0.52
The Danish reference pan genome	Danish	Study-wide	40	C=0.82	T=0.17
Siberian	Global	Study-wide	10	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 10	NC_000010.11:g.11742634C>T
GRCh37.p13 chr 10	NC_000010.10:g.11784633C>T

Gene: ECHDC3, enoyl-CoA hydratase domain containing 3 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ECHDC3 transcript	NM_024693.5:c.58C>T	R [CGC] > C [TGC]	Coding Sequence Variant
enoyl-CoA hydratase domain-containing protein 3, mitochondrial precursor	NP_078969.3:p.Arg20Cys	R (Arg) > C (Cys)	Missense Variant
ECHDC3 transcript variant X2	XM_011519689.1:c.58C>T	R [CGC] > C [TGC]	Coding Sequence Variant
enoyl-CoA hydratase domain-containing protein 3, mitochondrial isoform X2	XP_011517991.1:p.Arg20Cys	R (Arg) > C (Cys)	Missense Variant
ECHDC3 transcript variant X1	XM_047425750.1:c.58C>T	R [CGC] > C [TGC]	Coding Sequence Variant
enoyl-CoA hydratase domain-containing protein 3, mitochondrial isoform X1	XP_047281706.1:p.Arg20Cys	R (Arg) > C (Cys)	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.

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=	T
GRCh38.p14 chr 10	NC_000010.11:g.11742634=	NC_000010.11:g.11742634C>T
GRCh37.p13 chr 10	NC_000010.10:g.11784633=	NC_000010.10:g.11784633C>T
ECHDC3 transcript	NM_024693.5:c.58=	NM_024693.5:c.58C>T
ECHDC3 transcript	NM_024693.4:c.58=	NM_024693.4:c.58C>T
ECHDC3 transcript variant X1	XM_047425750.1:c.58=	XM_047425750.1:c.58C>T
ECHDC3 transcript variant X2	XM_011519689.1:c.58=	XM_011519689.1:c.58C>T
enoyl-CoA hydratase domain-containing protein 3, mitochondrial precursor	NP_078969.3:p.Arg20=	NP_078969.3:p.Arg20Cys
enoyl-CoA hydratase domain-containing protein 3, mitochondrial isoform X1	XP_047281706.1:p.Arg20=	XP_047281706.1:p.Arg20Cys
enoyl-CoA hydratase domain-containing protein 3, mitochondrial isoform X2	XP_011517991.1:p.Arg20=	XP_011517991.1:p.Arg20Cys
enoyl-CoA hydratase domain-containing protein 3, mitochondrial precursor	NP_078969.2:p.Arg20=	NP_078969.2:p.Arg20Cys

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#.

62 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	CGAP-GAI	ss16266375	Feb 28, 2004 (120)
2	BUSHMAN	ss201152145	Jul 04, 2010 (132)
3	1000GENOMES	ss224569801	Jul 14, 2010 (132)
4	1000GENOMES	ss235058506	Jul 15, 2010 (132)
5	EXOME_CHIP	ss491432478	May 04, 2012 (137)
6	SSMP	ss656281311	Apr 25, 2013 (138)
7	NHLBI-ESP	ss712934704	Apr 25, 2013 (138)
8	JMKIDD_LAB	ss974473865	Aug 21, 2014 (142)
9	EVA-GONL	ss987202790	Aug 21, 2014 (142)
10	JMKIDD_LAB	ss1067510826	Aug 21, 2014 (142)
11	1000GENOMES	ss1336299364	Aug 21, 2014 (142)
12	EVA_GENOME_DK	ss1574922186	Apr 01, 2015 (144)
13	EVA_DECODE	ss1596854071	Apr 01, 2015 (144)
14	EVA_UK10K_ALSPAC	ss1624003699	Apr 01, 2015 (144)
15	EVA_UK10K_TWINSUK	ss1666997732	Apr 01, 2015 (144)
16	EVA_EXAC	ss1689813796	Apr 01, 2015 (144)
17	WEILL_CORNELL_DGM	ss1930526005	Feb 12, 2016 (147)
18	JJLAB	ss2025987592	Sep 14, 2016 (149)
19	USC_VALOUEV	ss2154230823	Dec 20, 2016 (150)
20	HUMAN_LONGEVITY	ss2172709165	Dec 20, 2016 (150)
21	GNOMAD	ss2738108579	Nov 08, 2017 (151)
22	GNOMAD	ss2748345397	Nov 08, 2017 (151)
23	GNOMAD	ss2885574349	Nov 08, 2017 (151)
24	SWEGEN	ss3005947081	Nov 08, 2017 (151)
25	BIOINF_KMB_FNS_UNIBA	ss3026778738	Nov 08, 2017 (151)
26	CSHL	ss3348964956	Nov 08, 2017 (151)
27	OMUKHERJEE_ADBS	ss3646402704	Oct 12, 2018 (152)
28	EGCUT_WGS	ss3673476576	Jul 13, 2019 (153)
29	EVA_DECODE	ss3689293945	Jul 13, 2019 (153)
30	ACPOP	ss3737067789	Jul 13, 2019 (153)
31	EVA	ss3747754087	Jul 13, 2019 (153)
32	PACBIO	ss3786584472	Jul 13, 2019 (153)
33	PACBIO	ss3791776840	Jul 13, 2019 (153)
34	PACBIO	ss3796658676	Jul 13, 2019 (153)
35	KHV_HUMAN_GENOMES	ss3813115651	Jul 13, 2019 (153)
36	EVA	ss3824500259	Apr 26, 2020 (154)
37	EVA	ss3825771163	Apr 26, 2020 (154)
38	EVA	ss3831971754	Apr 26, 2020 (154)
39	EVA	ss3839517171	Apr 26, 2020 (154)
40	EVA	ss3844983532	Apr 26, 2020 (154)
41	SGDP_PRJ	ss3873546909	Apr 26, 2020 (154)
42	KRGDB	ss3921490015	Apr 26, 2020 (154)
43	KOGIC	ss3967213252	Apr 26, 2020 (154)
44	FSA-LAB	ss3983972861	Apr 26, 2021 (155)
45	EVA	ss3986476060	Apr 26, 2021 (155)
46	TOPMED	ss4842654935	Apr 26, 2021 (155)
47	TOMMO_GENOMICS	ss5196289755	Apr 26, 2021 (155)
48	EVA	ss5236881950	Apr 26, 2021 (155)
49	1000G_HIGH_COVERAGE	ss5282940210	Oct 16, 2022 (156)
50	EVA	ss5391632934	Oct 16, 2022 (156)
51	HUGCELL_USP	ss5478716456	Oct 16, 2022 (156)
52	EVA	ss5509904710	Oct 16, 2022 (156)
53	1000G_HIGH_COVERAGE	ss5576337590	Oct 16, 2022 (156)
54	EVA	ss5623948486	Oct 16, 2022 (156)
55	SANFORD_IMAGENETICS	ss5648687676	Oct 16, 2022 (156)
56	TOMMO_GENOMICS	ss5741144872	Oct 16, 2022 (156)
57	YY_MCH	ss5811200931	Oct 16, 2022 (156)
58	EVA	ss5823985242	Oct 16, 2022 (156)
59	EVA	ss5848293611	Oct 16, 2022 (156)
60	EVA	ss5877761152	Oct 16, 2022 (156)
61	EVA	ss5939973774	Oct 16, 2022 (156)
62	EVA	ss5980595227	Oct 16, 2022 (156)
63	1000Genomes	NC_000010.10 - 11784633	Oct 12, 2018 (152)
64	1000Genomes_30x	NC_000010.11 - 11742634	Oct 16, 2022 (156)
65	The Avon Longitudinal Study of Parents and Children	NC_000010.10 - 11784633	Oct 12, 2018 (152)
66	Genetic variation in the Estonian population	NC_000010.10 - 11784633	Oct 12, 2018 (152)
67	ExAC	NC_000010.10 - 11784633	Oct 12, 2018 (152)
68	The Danish reference pan genome	NC_000010.10 - 11784633	Apr 26, 2020 (154)
69	gnomAD - Genomes	NC_000010.11 - 11742634	Apr 26, 2021 (155)
70	gnomAD - Exomes	NC_000010.10 - 11784633	Jul 13, 2019 (153)
71	GO Exome Sequencing Project	NC_000010.10 - 11784633	Oct 12, 2018 (152)
72	KOREAN population from KRGDB	NC_000010.10 - 11784633	Apr 26, 2020 (154)
73	Korean Genome Project	NC_000010.11 - 11742634	Apr 26, 2020 (154)
74	Northern Sweden	NC_000010.10 - 11784633	Jul 13, 2019 (153)
75	Qatari	NC_000010.10 - 11784633	Apr 26, 2020 (154)
76	SGDP_PRJ	NC_000010.10 - 11784633	Apr 26, 2020 (154)
77	Siberian	NC_000010.10 - 11784633	Apr 26, 2020 (154)
78	8.3KJPN	NC_000010.10 - 11784633	Apr 26, 2021 (155)
79	14KJPN	NC_000010.11 - 11742634	Oct 16, 2022 (156)
80	TopMed	NC_000010.11 - 11742634	Apr 26, 2021 (155)
81	UK 10K study - Twins	NC_000010.10 - 11784633	Oct 12, 2018 (152)
82	ALFA	NC_000010.11 - 11742634	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
ss201152145, ss1596854071	NC_000010.9:11824638:C:T	NC_000010.11:11742633:C:T	(self)
48646770, 27033467, 19214824, 27626, 2034745, 7302280, 957982, 28667409, 10352654, 12567935, 25563889, 6747177, 54259062, 27033467, ss224569801, ss235058506, ss491432478, ss656281311, ss712934704, ss974473865, ss987202790, ss1067510826, ss1336299364, ss1574922186, ss1624003699, ss1666997732, ss1689813796, ss1930526005, ss2025987592, ss2154230823, ss2738108579, ss2748345397, ss2885574349, ss3005947081, ss3348964956, ss3646402704, ss3673476576, ss3737067789, ss3747754087, ss3786584472, ss3791776840, ss3796658676, ss3824500259, ss3825771163, ss3831971754, ss3839517171, ss3873546909, ss3921490015, ss3983972861, ss3986476060, ss5196289755, ss5391632934, ss5509904710, ss5623948486, ss5648687676, ss5823985242, ss5848293611, ss5939973774, ss5980595227	NC_000010.10:11784632:C:T	NC_000010.11:11742633:C:T	(self)
63863525, 343616735, 23591253, 74981976, 58200590, 11294168263, ss2172709165, ss3026778738, ss3689293945, ss3813115651, ss3844983532, ss3967213252, ss4842654935, ss5236881950, ss5282940210, ss5478716456, ss5576337590, ss5741144872, ss5811200931, ss5877761152	NC_000010.11:11742633:C:T	NC_000010.11:11742633:C:T	(self)
ss16266375	NT_008705.16:11724632:C:T	NC_000010.11:11742633: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 rs11558855

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

rs11558855