Name: rs56207008
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.

rs56207008

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr11:64115743 (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: T=0.106506 (28191/264690, TOPMED)
T=0.111381 (15610/140150, GnomAD)
T=0.16721 (4725/28258, 14KJPN) (+ 16 more)
T=0.12544 (2341/18662, ALFA)
T=0.16881 (2829/16758, 8.3KJPN)
T=0.0765 (490/6404, 1000G_30x)
T=0.0773 (387/5008, 1000G)
T=0.1292 (579/4480, Estonian)
T=0.1694 (653/3854, ALSPAC)
T=0.1761 (653/3708, TWINSUK)
T=0.1331 (390/2930, KOREAN)
T=0.1316 (241/1832, Korea1K)
T=0.178 (178/998, GoNL)
T=0.183 (110/600, NorthernSweden)
T=0.028 (6/216, Qatari)
T=0.086 (18/210, Vietnamese)
C=0.47 (45/96, SGDP_PRJ)
T=0.15 (6/40, GENOME_DK)
C=0.38 (6/16, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: FLRT1 : Intron Variant
MACROD1 : 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	18662	C=0.87456	A=0.00000, T=0.12544
European	Sub	14094	C=0.85455	A=0.00000, T=0.14545
African	Sub	2912	C=0.9533	A=0.0000, T=0.0467
African Others	Sub	112	C=0.973	A=0.000, T=0.027
African American	Sub	2800	C=0.9525	A=0.0000, T=0.0475
Asian	Sub	112	C=0.991	A=0.000, T=0.009
East Asian	Sub	86	C=0.99	A=0.00, T=0.01
Other Asian	Sub	26	C=1.00	A=0.00, T=0.00
Latin American 1	Sub	146	C=0.938	A=0.000, T=0.062
Latin American 2	Sub	610	C=0.905	A=0.000, T=0.095
South Asian	Sub	98	C=0.94	A=0.00, T=0.06
Other	Sub	690	C=0.883	A=0.000, T=0.117

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=0.893494	T=0.106506
gnomAD - Genomes	Global	Study-wide	140150	C=0.888619	T=0.111381
gnomAD - Genomes	European	Sub	75876	C=0.84527	T=0.15473
gnomAD - Genomes	African	Sub	42026	C=0.95662	T=0.04338
gnomAD - Genomes	American	Sub	13642	C=0.90639	T=0.09361
gnomAD - Genomes	Ashkenazi Jewish	Sub	3318	C=0.9253	T=0.0747
gnomAD - Genomes	East Asian	Sub	3134	C=0.9043	T=0.0957
gnomAD - Genomes	Other	Sub	2154	C=0.8969	T=0.1031
14KJPN	JAPANESE	Study-wide	28258	C=0.83279	T=0.16721
Allele Frequency Aggregator	Total	Global	18662	C=0.87456	A=0.00000, T=0.12544
Allele Frequency Aggregator	European	Sub	14094	C=0.85455	A=0.00000, T=0.14545
Allele Frequency Aggregator	African	Sub	2912	C=0.9533	A=0.0000, T=0.0467
Allele Frequency Aggregator	Other	Sub	690	C=0.883	A=0.000, T=0.117
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.905	A=0.000, T=0.095
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.938	A=0.000, T=0.062
Allele Frequency Aggregator	Asian	Sub	112	C=0.991	A=0.000, T=0.009
Allele Frequency Aggregator	South Asian	Sub	98	C=0.94	A=0.00, T=0.06
8.3KJPN	JAPANESE	Study-wide	16758	C=0.83119	T=0.16881
1000Genomes_30x	Global	Study-wide	6404	C=0.9235	T=0.0765
1000Genomes_30x	African	Sub	1786	C=0.9759	T=0.0241
1000Genomes_30x	Europe	Sub	1266	C=0.8539	T=0.1461
1000Genomes_30x	South Asian	Sub	1202	C=0.9285	T=0.0715
1000Genomes_30x	East Asian	Sub	1170	C=0.9197	T=0.0803
1000Genomes_30x	American	Sub	980	C=0.916	T=0.084
1000Genomes	Global	Study-wide	5008	C=0.9227	T=0.0773
1000Genomes	African	Sub	1322	C=0.9735	T=0.0265
1000Genomes	East Asian	Sub	1008	C=0.9206	T=0.0794
1000Genomes	Europe	Sub	1006	C=0.8588	T=0.1412
1000Genomes	South Asian	Sub	978	C=0.927	T=0.073
1000Genomes	American	Sub	694	C=0.915	T=0.085
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.8708	T=0.1292
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.8306	T=0.1694
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.8239	T=0.1761
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.8669	T=0.1331
Korean Genome Project	KOREAN	Study-wide	1832	C=0.8684	T=0.1316
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.822	T=0.178
Northern Sweden	ACPOP	Study-wide	600	C=0.817	T=0.183
Qatari	Global	Study-wide	216	C=0.972	T=0.028
A Vietnamese Genetic Variation Database	Global	Study-wide	210	C=0.914	T=0.086
SGDP_PRJ	Global	Study-wide	96	C=0.47	T=0.53
The Danish reference pan genome	Danish	Study-wide	40	C=0.85	T=0.15
Siberian	Global	Study-wide	16	C=0.38	T=0.62

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 11	NC_000011.10:g.64115743C>A
GRCh38.p14 chr 11	NC_000011.10:g.64115743C>G
GRCh38.p14 chr 11	NC_000011.10:g.64115743C>T
GRCh37.p13 chr 11	NC_000011.9:g.63883215C>A
GRCh37.p13 chr 11	NC_000011.9:g.63883215C>G
GRCh37.p13 chr 11	NC_000011.9:g.63883215C>T

Gene: FLRT1, fibronectin leucine rich transmembrane protein 1 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
FLRT1 transcript variant 2	NM_001384466.1:c.-49-476C… NM_001384466.1:c.-49-476C>A	N/A	Intron Variant
FLRT1 transcript variant 1	NM_013280.5:c.-49-476C>A	N/A	Intron Variant
FLRT1 transcript variant X2	XM_047426697.1:c.-49-476C… XM_047426697.1:c.-49-476C>A	N/A	Intron Variant
FLRT1 transcript variant X4	XM_047426699.1:c.-49-476C… XM_047426699.1:c.-49-476C>A	N/A	Intron Variant
FLRT1 transcript variant X1	XM_047426696.1:c.-431=	N/A	5 Prime UTR Variant
FLRT1 transcript variant X3	XM_047426698.1:c.-431=	N/A	5 Prime UTR Variant

Gene: MACROD1, mono-ADP ribosylhydrolase 1 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
MACROD1 transcript variant 1	NM_014067.4:c.517+35496G>T	N/A	Intron Variant
MACROD1 transcript variant X1	XM_005273939.5:c.517+3549… XM_005273939.5:c.517+35496G>T	N/A	Intron Variant
MACROD1 transcript variant X1	XM_011544970.3:c.517+3549… XM_011544970.3:c.517+35496G>T	N/A	Intron Variant
MACROD1 transcript variant X2	XM_006718521.4:c.*164=	N/A	3 Prime UTR Variant
MACROD1 transcript variant X3	XM_005273940.3:c.	N/A	Genic Downstream Transcript Variant
MACROD1 transcript variant X4	XM_006718522.3:c.	N/A	Genic Downstream Transcript 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 11	NC_000011.10:g.64115743=	NC_000011.10:g.64115743C>A	NC_000011.10:g.64115743C>G	NC_000011.10:g.64115743C>T
GRCh37.p13 chr 11	NC_000011.9:g.63883215=	NC_000011.9:g.63883215C>A	NC_000011.9:g.63883215C>G	NC_000011.9:g.63883215C>T
MACROD1 transcript variant X2	XM_006718521.4:c.*164=	XM_006718521.4:c.*164G>T	XM_006718521.4:c.*164G>C	XM_006718521.4:c.*164G>A
MACROD1 transcript variant X3	XM_006718521.3:c.*164=	XM_006718521.3:c.*164G>T	XM_006718521.3:c.*164G>C	XM_006718521.3:c.*164G>A
MACROD1 transcript variant X4	XM_006718521.2:c.*164=	XM_006718521.2:c.*164G>T	XM_006718521.2:c.*164G>C	XM_006718521.2:c.*164G>A
MACROD1 transcript variant X4	XM_006718521.1:c.*164=	XM_006718521.1:c.*164G>T	XM_006718521.1:c.*164G>C	XM_006718521.1:c.*164G>A
FLRT1 transcript variant X3	XM_047426698.1:c.-431=	XM_047426698.1:c.-431C>A	XM_047426698.1:c.-431C>G	XM_047426698.1:c.-431C>T
FLRT1 transcript variant X1	XM_047426696.1:c.-431=	XM_047426696.1:c.-431C>A	XM_047426696.1:c.-431C>G	XM_047426696.1:c.-431C>T
FLRT1 transcript variant 2	NM_001384466.1:c.-49-476=	NM_001384466.1:c.-49-476C>A	NM_001384466.1:c.-49-476C>G	NM_001384466.1:c.-49-476C>T
FLRT1 transcript	NM_013280.4:c.-49-476=	NM_013280.4:c.-49-476C>A	NM_013280.4:c.-49-476C>G	NM_013280.4:c.-49-476C>T
FLRT1 transcript variant 1	NM_013280.5:c.-49-476=	NM_013280.5:c.-49-476C>A	NM_013280.5:c.-49-476C>G	NM_013280.5:c.-49-476C>T
MACROD1 transcript	NM_014067.3:c.517+35496=	NM_014067.3:c.517+35496G>T	NM_014067.3:c.517+35496G>C	NM_014067.3:c.517+35496G>A
MACROD1 transcript variant 1	NM_014067.4:c.517+35496=	NM_014067.4:c.517+35496G>T	NM_014067.4:c.517+35496G>C	NM_014067.4:c.517+35496G>A
FLRT1 transcript variant X1	XM_005273861.1:c.-49-476=	XM_005273861.1:c.-49-476C>A	XM_005273861.1:c.-49-476C>G	XM_005273861.1:c.-49-476C>T
MACROD1 transcript variant X1	XM_005273939.1:c.517+35496=	XM_005273939.1:c.517+35496G>T	XM_005273939.1:c.517+35496G>C	XM_005273939.1:c.517+35496G>A
MACROD1 transcript variant X1	XM_005273939.5:c.517+35496=	XM_005273939.5:c.517+35496G>T	XM_005273939.5:c.517+35496G>C	XM_005273939.5:c.517+35496G>A
MACROD1 transcript variant X1	XM_011544970.3:c.517+35496=	XM_011544970.3:c.517+35496G>T	XM_011544970.3:c.517+35496G>C	XM_011544970.3:c.517+35496G>A
FLRT1 transcript variant X2	XM_047426697.1:c.-49-476=	XM_047426697.1:c.-49-476C>A	XM_047426697.1:c.-49-476C>G	XM_047426697.1:c.-49-476C>T
FLRT1 transcript variant X4	XM_047426699.1:c.-49-476=	XM_047426699.1:c.-49-476C>A	XM_047426699.1:c.-49-476C>G	XM_047426699.1:c.-49-476C>T

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#.

55 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	HGSV	ss78650874	Dec 07, 2007 (129)
2	BGI	ss102971558	Dec 01, 2009 (131)
3	1000GENOMES	ss110575844	Jan 25, 2009 (130)
4	GMI	ss156401974	Dec 01, 2009 (131)
5	COMPLETE_GENOMICS	ss168482955	Jul 04, 2010 (132)
6	1000GENOMES	ss225281489	Jul 14, 2010 (132)
7	1000GENOMES	ss235589664	Jul 15, 2010 (132)
8	1000GENOMES	ss242214890	Jul 15, 2010 (132)
9	BL	ss255226751	May 09, 2011 (134)
10	GMI	ss281039820	May 04, 2012 (137)
11	GMI	ss286396312	Apr 25, 2013 (138)
12	TISHKOFF	ss562607916	Apr 25, 2013 (138)
13	SSMP	ss658119766	Apr 25, 2013 (138)
14	EVA-GONL	ss988604034	Aug 21, 2014 (142)
15	JMKIDD_LAB	ss1077788169	Aug 21, 2014 (142)
16	1000GENOMES	ss1341591501	Aug 21, 2014 (142)
17	EVA_GENOME_DK	ss1575757475	Apr 01, 2015 (144)
18	EVA_DECODE	ss1598266219	Apr 01, 2015 (144)
19	EVA_UK10K_ALSPAC	ss1626753970	Apr 01, 2015 (144)
20	EVA_UK10K_TWINSUK	ss1669748003	Apr 01, 2015 (144)
21	WEILL_CORNELL_DGM	ss1931962937	Feb 12, 2016 (147)
22	JJLAB	ss2026727702	Sep 14, 2016 (149)
23	ILLUMINA	ss2095023133	Dec 20, 2016 (150)
24	USC_VALOUEV	ss2155031317	Dec 20, 2016 (150)
25	HUMAN_LONGEVITY	ss2182982173	Dec 20, 2016 (150)
26	GRF	ss2699321747	Nov 08, 2017 (151)
27	GNOMAD	ss2900561862	Nov 08, 2017 (151)
28	SWEGEN	ss3008225303	Nov 08, 2017 (151)
29	BIOINF_KMB_FNS_UNIBA	ss3027162222	Nov 08, 2017 (151)
30	CSHL	ss3349636291	Nov 08, 2017 (151)
31	ILLUMINA	ss3651708214	Oct 12, 2018 (152)
32	EGCUT_WGS	ss3675562026	Jul 13, 2019 (153)
33	EVA_DECODE	ss3691939194	Jul 13, 2019 (153)
34	ACPOP	ss3738246696	Jul 13, 2019 (153)
35	EVA	ss3749392671	Jul 13, 2019 (153)
36	KHV_HUMAN_GENOMES	ss3814736246	Jul 13, 2019 (153)
37	EVA	ss3832668312	Apr 26, 2020 (154)
38	EVA	ss3839891726	Apr 26, 2020 (154)
39	EVA	ss3845371145	Apr 26, 2020 (154)
40	SGDP_PRJ	ss3876421905	Apr 26, 2020 (154)
41	KRGDB	ss3924793786	Apr 26, 2020 (154)
42	KOGIC	ss3970058060	Apr 26, 2020 (154)
43	TOPMED	ss4888012084	Apr 26, 2021 (155)
44	TOMMO_GENOMICS	ss5202339212	Apr 26, 2021 (155)
45	1000G_HIGH_COVERAGE	ss5287696639	Oct 16, 2022 (156)
46	EVA	ss5400070473	Oct 16, 2022 (156)
47	HUGCELL_USP	ss5482842899	Oct 16, 2022 (156)
48	EVA	ss5510391687	Oct 16, 2022 (156)
49	1000G_HIGH_COVERAGE	ss5583560755	Oct 16, 2022 (156)
50	SANFORD_IMAGENETICS	ss5651382502	Oct 16, 2022 (156)
51	TOMMO_GENOMICS	ss5750325705	Oct 16, 2022 (156)
52	YY_MCH	ss5812482392	Oct 16, 2022 (156)
53	EVA	ss5836768444	Oct 16, 2022 (156)
54	EVA	ss5920290250	Oct 16, 2022 (156)
55	EVA	ss5942695295	Oct 16, 2022 (156)
56	1000Genomes	NC_000011.9 - 63883215	Oct 12, 2018 (152)
57	1000Genomes_30x	NC_000011.10 - 64115743	Oct 16, 2022 (156)
58	The Avon Longitudinal Study of Parents and Children	NC_000011.9 - 63883215	Oct 12, 2018 (152)
59	Genetic variation in the Estonian population	NC_000011.9 - 63883215	Oct 12, 2018 (152)
60	The Danish reference pan genome	NC_000011.9 - 63883215	Apr 26, 2020 (154)
61	gnomAD - Genomes	NC_000011.10 - 64115743	Apr 26, 2021 (155)
62	Genome of the Netherlands Release 5	NC_000011.9 - 63883215	Apr 26, 2020 (154)
63	KOREAN population from KRGDB	NC_000011.9 - 63883215	Apr 26, 2020 (154)
64	Korean Genome Project	NC_000011.10 - 64115743	Apr 26, 2020 (154)
65	Northern Sweden	NC_000011.9 - 63883215	Jul 13, 2019 (153)
66	Qatari	NC_000011.9 - 63883215	Apr 26, 2020 (154)
67	SGDP_PRJ	NC_000011.9 - 63883215	Apr 26, 2020 (154)
68	Siberian	NC_000011.9 - 63883215	Apr 26, 2020 (154)
69	8.3KJPN	NC_000011.9 - 63883215	Apr 26, 2021 (155)
70	14KJPN	NC_000011.10 - 64115743	Oct 16, 2022 (156)
71	TopMed	NC_000011.10 - 64115743	Apr 26, 2021 (155)
72	UK 10K study - Twins	NC_000011.9 - 63883215	Oct 12, 2018 (152)
73	A Vietnamese Genetic Variation Database	NC_000011.9 - 63883215	Jul 13, 2019 (153)
74	ALFA	NC_000011.10 - 64115743	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
5212169443	NC_000011.10:64115742:C:A	NC_000011.10:64115742:C:A	(self)
ss2182982173	NC_000011.10:64115742:C:G	NC_000011.10:64115742:C:G	(self)
ss78650874, ss110575844, ss168482955, ss255226751, ss281039820, ss286396312, ss1598266219	NC_000011.8:63639790:C:T	NC_000011.10:64115742:C:T	(self)
54124985, 30054231, 21300274, 2599095, 13412002, 31971180, 11531561, 14004867, 28438885, 7547671, 60308519, 30054231, 6671148, ss225281489, ss235589664, ss242214890, ss562607916, ss658119766, ss988604034, ss1077788169, ss1341591501, ss1575757475, ss1626753970, ss1669748003, ss1931962937, ss2026727702, ss2095023133, ss2155031317, ss2699321747, ss2900561862, ss3008225303, ss3349636291, ss3651708214, ss3675562026, ss3738246696, ss3749392671, ss3832668312, ss3839891726, ss3876421905, ss3924793786, ss5202339212, ss5400070473, ss5510391687, ss5651382502, ss5836768444, ss5942695295	NC_000011.9:63883214:C:T	NC_000011.10:64115742:C:T	(self)
71086690, 382034456, 26436061, 84162809, 103557740, 5212169443, ss2182982173, ss3027162222, ss3691939194, ss3814736246, ss3845371145, ss3970058060, ss4888012084, ss5287696639, ss5482842899, ss5583560755, ss5750325705, ss5812482392, ss5920290250	NC_000011.10:64115742:C:T	NC_000011.10:64115742:C:T	(self)
ss102971558, ss156401974	NT_167190.1:9189009:C:T	NC_000011.10:64115742: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 rs56207008

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

rs56207008