Name: rs10025977
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.

rs10025977

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:78119825 (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: T>C
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.165148 (43713/264690, TOPMED)
C=0.171887 (24079/140086, GnomAD)
C=0.17951 (12817/71400, ALFA) (+ 19 more)
C=0.05747 (1624/28258, 14KJPN)
C=0.05656 (948/16760, 8.3KJPN)
C=0.1337 (856/6404, 1000G_30x)
C=0.1306 (654/5008, 1000G)
C=0.2232 (1000/4480, Estonian)
C=0.2042 (787/3854, ALSPAC)
C=0.1880 (697/3708, TWINSUK)
C=0.0590 (173/2930, KOREAN)
C=0.1281 (267/2084, HGDP_Stanford)
C=0.1229 (232/1888, HapMap)
C=0.0639 (117/1832, Korea1K)
C=0.209 (209/998, GoNL)
C=0.195 (117/600, NorthernSweden)
C=0.093 (20/216, Qatari)
C=0.065 (14/216, Vietnamese)
T=0.443 (54/122, SGDP_PRJ)
C=0.15 (6/40, GENOME_DK)
C=0.00 (0/36, Ancient Sardinia)
T=0.44 (8/18, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: FRAS1 : 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	71400	T=0.82049	C=0.17951
European	Sub	58772	T=0.80596	C=0.19404
African	Sub	4526	T=0.8807	C=0.1193
African Others	Sub	170	T=0.941	C=0.059
African American	Sub	4356	T=0.8783	C=0.1217
Asian	Sub	190	T=0.947	C=0.053
East Asian	Sub	148	T=0.939	C=0.061
Other Asian	Sub	42	T=0.98	C=0.02
Latin American 1	Sub	254	T=0.862	C=0.138
Latin American 2	Sub	1232	T=0.8019	C=0.1981
South Asian	Sub	4956	T=0.9314	C=0.0686
Other	Sub	1470	T=0.8340	C=0.1660

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").

Download

Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	T=0.834852	C=0.165148
gnomAD - Genomes	Global	Study-wide	140086	T=0.828113	C=0.171887
gnomAD - Genomes	European	Sub	75848	T=0.79970	C=0.20030
gnomAD - Genomes	African	Sub	41996	T=0.87730	C=0.12270
gnomAD - Genomes	American	Sub	13640	T=0.79443	C=0.20557
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	T=0.8788	C=0.1212
gnomAD - Genomes	East Asian	Sub	3130	T=0.9514	C=0.0486
gnomAD - Genomes	Other	Sub	2148	T=0.8254	C=0.1746
Allele Frequency Aggregator	Total	Global	71400	T=0.82049	C=0.17951
Allele Frequency Aggregator	European	Sub	58772	T=0.80596	C=0.19404
Allele Frequency Aggregator	South Asian	Sub	4956	T=0.9314	C=0.0686
Allele Frequency Aggregator	African	Sub	4526	T=0.8807	C=0.1193
Allele Frequency Aggregator	Other	Sub	1470	T=0.8340	C=0.1660
Allele Frequency Aggregator	Latin American 2	Sub	1232	T=0.8019	C=0.1981
Allele Frequency Aggregator	Latin American 1	Sub	254	T=0.862	C=0.138
Allele Frequency Aggregator	Asian	Sub	190	T=0.947	C=0.053
14KJPN	JAPANESE	Study-wide	28258	T=0.94253	C=0.05747
8.3KJPN	JAPANESE	Study-wide	16760	T=0.94344	C=0.05656
1000Genomes_30x	Global	Study-wide	6404	T=0.8663	C=0.1337
1000Genomes_30x	African	Sub	1786	T=0.8768	C=0.1232
1000Genomes_30x	Europe	Sub	1266	T=0.8002	C=0.1998
1000Genomes_30x	South Asian	Sub	1202	T=0.9060	C=0.0940
1000Genomes_30x	East Asian	Sub	1170	T=0.9462	C=0.0538
1000Genomes_30x	American	Sub	980	T=0.789	C=0.211
1000Genomes	Global	Study-wide	5008	T=0.8694	C=0.1306
1000Genomes	African	Sub	1322	T=0.8729	C=0.1271
1000Genomes	East Asian	Sub	1008	T=0.9474	C=0.0526
1000Genomes	Europe	Sub	1006	T=0.7992	C=0.2008
1000Genomes	South Asian	Sub	978	T=0.908	C=0.092
1000Genomes	American	Sub	694	T=0.797	C=0.203
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.7768	C=0.2232
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.7958	C=0.2042
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.8120	C=0.1880
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.9410	C=0.0590
HGDP-CEPH-db Supplement 1	Global	Study-wide	2084	T=0.8719	C=0.1281
HGDP-CEPH-db Supplement 1	Est_Asia	Sub	470	T=0.917	C=0.083
HGDP-CEPH-db Supplement 1	Central_South_Asia	Sub	414	T=0.940	C=0.060
HGDP-CEPH-db Supplement 1	Middle_Est	Sub	350	T=0.831	C=0.169
HGDP-CEPH-db Supplement 1	Europe	Sub	320	T=0.834	C=0.166
HGDP-CEPH-db Supplement 1	Africa	Sub	242	T=0.946	C=0.054
HGDP-CEPH-db Supplement 1	America	Sub	216	T=0.657	C=0.343
HGDP-CEPH-db Supplement 1	Oceania	Sub	72	T=0.94	C=0.06
HapMap	Global	Study-wide	1888	T=0.8771	C=0.1229
HapMap	American	Sub	768	T=0.863	C=0.137
HapMap	African	Sub	692	T=0.880	C=0.120
HapMap	Asian	Sub	252	T=0.948	C=0.052
HapMap	Europe	Sub	176	T=0.824	C=0.176
Korean Genome Project	KOREAN	Study-wide	1832	T=0.9361	C=0.0639
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.791	C=0.209
Northern Sweden	ACPOP	Study-wide	600	T=0.805	C=0.195
Qatari	Global	Study-wide	216	T=0.907	C=0.093
A Vietnamese Genetic Variation Database	Global	Study-wide	216	T=0.935	C=0.065
SGDP_PRJ	Global	Study-wide	122	T=0.443	C=0.557
The Danish reference pan genome	Danish	Study-wide	40	T=0.85	C=0.15
Ancient Sardinia genome-wide 1240k capture data generation and analysis	Global	Study-wide	36	T=1.00	C=0.00
Siberian	Global	Study-wide	18	T=0.44	C=0.56

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.78119825T>C
GRCh37.p13 chr 4	NC_000004.11:g.79040979T>C
FRAS1 RefSeqGene	NG_015812.2:g.67256T>C

Gene: FRAS1, Fraser extracellular matrix complex subunit 1 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
FRAS1 transcript variant 2	NM_001166133.2:c.108+5380… NM_001166133.2:c.108+53809T>C	N/A	Intron Variant
FRAS1 transcript variant 1	NM_025074.7:c.108+53809T>C	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	T=	C
GRCh38.p14 chr 4	NC_000004.12:g.78119825=	NC_000004.12:g.78119825T>C
GRCh37.p13 chr 4	NC_000004.11:g.79040979=	NC_000004.11:g.79040979T>C
FRAS1 RefSeqGene	NG_015812.2:g.67256=	NG_015812.2:g.67256T>C
FRAS1 transcript variant 2	NM_001166133.1:c.108+53809=	NM_001166133.1:c.108+53809T>C
FRAS1 transcript variant 2	NM_001166133.2:c.108+53809=	NM_001166133.2:c.108+53809T>C
FRAS1 transcript variant 1	NM_025074.6:c.108+53809=	NM_025074.6:c.108+53809T>C
FRAS1 transcript variant 1	NM_025074.7:c.108+53809=	NM_025074.7:c.108+53809T>C

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#.

81 SubSNP, 22 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	WI_SSAHASNP	ss13872783	Dec 05, 2003 (119)
2	ILLUMINA	ss66539195	Nov 29, 2006 (127)
3	ILLUMINA	ss66865100	Nov 29, 2006 (127)
4	ILLUMINA	ss66935596	Nov 29, 2006 (127)
5	CSHL-HAPMAP	ss68421994	Jan 12, 2007 (127)
6	ILLUMINA	ss70356550	May 16, 2007 (127)
7	ILLUMINA	ss70460472	May 25, 2008 (130)
8	ILLUMINA	ss70981164	May 16, 2007 (127)
9	ILLUMINA	ss75326920	Dec 07, 2007 (129)
10	KRIBB_YJKIM	ss84891996	Dec 15, 2007 (130)
11	HUMANGENOME_JCVI	ss98973569	Feb 06, 2009 (130)
12	1000GENOMES	ss108069227	Jan 22, 2009 (130)
13	ILLUMINA-UK	ss117059456	Feb 14, 2009 (130)
14	ILLUMINA	ss121254302	Dec 01, 2009 (131)
15	ENSEMBL	ss143781812	Dec 01, 2009 (131)
16	ILLUMINA	ss152545437	Dec 01, 2009 (131)
17	ILLUMINA	ss159104384	Dec 01, 2009 (131)
18	ILLUMINA	ss169217742	Jul 04, 2010 (132)
19	ILLUMINA	ss169531092	Jul 04, 2010 (132)
20	1000GENOMES	ss211436380	Jul 14, 2010 (132)
21	1000GENOMES	ss221017949	Jul 14, 2010 (132)
22	1000GENOMES	ss232458410	Jul 14, 2010 (132)
23	1000GENOMES	ss239738111	Jul 15, 2010 (132)
24	GMI	ss277790203	May 04, 2012 (137)
25	PJP	ss293108191	May 09, 2011 (134)
26	ILLUMINA	ss536566900	Sep 08, 2015 (146)
27	TISHKOFF	ss557623747	Apr 25, 2013 (138)
28	SSMP	ss651431719	Apr 25, 2013 (138)
29	ILLUMINA	ss825326281	Jul 19, 2016 (147)
30	ILLUMINA	ss832617177	Jul 13, 2019 (153)
31	EVA-GONL	ss980290021	Aug 21, 2014 (142)
32	JMKIDD_LAB	ss1071670953	Aug 21, 2014 (142)
33	1000GENOMES	ss1310397802	Aug 21, 2014 (142)
34	EVA_GENOME_DK	ss1580627590	Apr 01, 2015 (144)
35	EVA_DECODE	ss1589790114	Apr 01, 2015 (144)
36	EVA_UK10K_ALSPAC	ss1610424168	Apr 01, 2015 (144)
37	EVA_UK10K_TWINSUK	ss1653418201	Apr 01, 2015 (144)
38	EVA_SVP	ss1712683355	Apr 01, 2015 (144)
39	WEILL_CORNELL_DGM	ss1923532971	Feb 12, 2016 (147)
40	JJLAB	ss2022352384	Sep 14, 2016 (149)
41	USC_VALOUEV	ss2150480978	Dec 20, 2016 (150)
42	HUMAN_LONGEVITY	ss2264197291	Dec 20, 2016 (150)
43	SYSTEMSBIOZJU	ss2625677547	Nov 08, 2017 (151)
44	GRF	ss2705955873	Nov 08, 2017 (151)
45	GNOMAD	ss2811176815	Nov 08, 2017 (151)
46	SWEGEN	ss2994970617	Nov 08, 2017 (151)
47	BIOINF_KMB_FNS_UNIBA	ss3024951195	Nov 08, 2017 (151)
48	CSHL	ss3345796014	Nov 08, 2017 (151)
49	ILLUMINA	ss3628996747	Oct 12, 2018 (152)
50	ILLUMINA	ss3638494296	Oct 12, 2018 (152)
51	ILLUMINA	ss3639249741	Oct 12, 2018 (152)
52	ILLUMINA	ss3639646050	Oct 12, 2018 (152)
53	ILLUMINA	ss3643445008	Oct 12, 2018 (152)
54	URBANLAB	ss3647770236	Oct 12, 2018 (152)
55	EGCUT_WGS	ss3662854403	Jul 13, 2019 (153)
56	EVA_DECODE	ss3712370612	Jul 13, 2019 (153)
57	ACPOP	ss3731295222	Jul 13, 2019 (153)
58	EVA	ss3761997101	Jul 13, 2019 (153)
59	KHV_HUMAN_GENOMES	ss3805138878	Jul 13, 2019 (153)
60	EVA	ss3828628189	Apr 26, 2020 (154)
61	EVA	ss3837755615	Apr 26, 2020 (154)
62	EVA	ss3843193132	Apr 26, 2020 (154)
63	HGDP	ss3847754679	Apr 26, 2020 (154)
64	SGDP_PRJ	ss3859302787	Apr 26, 2020 (154)
65	KRGDB	ss3905563717	Apr 26, 2020 (154)
66	KOGIC	ss3954479157	Apr 26, 2020 (154)
67	EVA	ss3985077618	Apr 26, 2021 (155)
68	EVA	ss4017152819	Apr 26, 2021 (155)
69	TOPMED	ss4619497763	Apr 26, 2021 (155)
70	TOMMO_GENOMICS	ss5166439158	Apr 26, 2021 (155)
71	1000G_HIGH_COVERAGE	ss5259777268	Oct 13, 2022 (156)
72	EVA	ss5350044783	Oct 13, 2022 (156)
73	HUGCELL_USP	ss5458473442	Oct 13, 2022 (156)
74	EVA	ss5507582747	Oct 13, 2022 (156)
75	1000G_HIGH_COVERAGE	ss5541168852	Oct 13, 2022 (156)
76	SANFORD_IMAGENETICS	ss5635369906	Oct 13, 2022 (156)
77	TOMMO_GENOMICS	ss5700987262	Oct 13, 2022 (156)
78	YY_MCH	ss5805230936	Oct 13, 2022 (156)
79	EVA	ss5844220352	Oct 13, 2022 (156)
80	EVA	ss5864095938	Oct 13, 2022 (156)
81	EVA	ss5963749121	Oct 13, 2022 (156)
82	1000Genomes	NC_000004.11 - 79040979	Oct 12, 2018 (152)
83	1000Genomes_30x	NC_000004.12 - 78119825	Oct 13, 2022 (156)
84	The Avon Longitudinal Study of Parents and Children	NC_000004.11 - 79040979	Oct 12, 2018 (152)
85	Genetic variation in the Estonian population	NC_000004.11 - 79040979	Oct 12, 2018 (152)
86	The Danish reference pan genome	NC_000004.11 - 79040979	Apr 26, 2020 (154)
87	gnomAD - Genomes	NC_000004.12 - 78119825	Apr 26, 2021 (155)
88	Genome of the Netherlands Release 5	NC_000004.11 - 79040979	Apr 26, 2020 (154)
89	HGDP-CEPH-db Supplement 1	NC_000004.10 - 79260003	Apr 26, 2020 (154)
90	HapMap	NC_000004.12 - 78119825	Apr 26, 2020 (154)
91	KOREAN population from KRGDB	NC_000004.11 - 79040979	Apr 26, 2020 (154)
92	Korean Genome Project	NC_000004.12 - 78119825	Apr 26, 2020 (154)
93	Northern Sweden	NC_000004.11 - 79040979	Jul 13, 2019 (153)
94	Ancient Sardinia genome-wide 1240k capture data generation and analysis	NC_000004.11 - 79040979	Apr 26, 2021 (155)
95	Qatari	NC_000004.11 - 79040979	Apr 26, 2020 (154)
96	SGDP_PRJ	NC_000004.11 - 79040979	Apr 26, 2020 (154)
97	Siberian	NC_000004.11 - 79040979	Apr 26, 2020 (154)
98	8.3KJPN	NC_000004.11 - 79040979	Apr 26, 2021 (155)
99	14KJPN	NC_000004.12 - 78119825	Oct 13, 2022 (156)
100	TopMed	NC_000004.12 - 78119825	Apr 26, 2021 (155)
101	UK 10K study - Twins	NC_000004.11 - 79040979	Oct 12, 2018 (152)
102	A Vietnamese Genetic Variation Database	NC_000004.11 - 79040979	Jul 13, 2019 (153)
103	ALFA	NC_000004.12 - 78119825	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).

Associated ID	History Updated (Build)
rs60107840	May 25, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss3639249741, ss3639646050	NC_000004.9:79398157:T:C	NC_000004.12:78119824:T:C	(self)
432571, ss108069227, ss117059456, ss211436380, ss277790203, ss293108191, ss825326281, ss1589790114, ss1712683355, ss3643445008, ss3847754679	NC_000004.10:79260002:T:C	NC_000004.12:78119824:T:C	(self)
21817170, 12129711, 8592651, 6792529, 5357326, 12741111, 4580087, 303545, 5574901, 11319767, 2997332, 24408465, 12129711, 2671390, ss221017949, ss232458410, ss239738111, ss536566900, ss557623747, ss651431719, ss832617177, ss980290021, ss1071670953, ss1310397802, ss1580627590, ss1610424168, ss1653418201, ss1923532971, ss2022352384, ss2150480978, ss2625677547, ss2705955873, ss2811176815, ss2994970617, ss3345796014, ss3628996747, ss3638494296, ss3662854403, ss3731295222, ss3761997101, ss3828628189, ss3837755615, ss3859302787, ss3905563717, ss3985077618, ss4017152819, ss5166439158, ss5350044783, ss5507582747, ss5635369906, ss5844220352, ss5963749121	NC_000004.11:79040978:T:C	NC_000004.12:78119824:T:C	(self)
28694787, 154540072, 2643768, 10857158, 34824366, 456875319, 1091185832, ss2264197291, ss3024951195, ss3647770236, ss3712370612, ss3805138878, ss3843193132, ss3954479157, ss4619497763, ss5259777268, ss5458473442, ss5541168852, ss5700987262, ss5805230936, ss5864095938	NC_000004.12:78119824:T:C	NC_000004.12:78119824:T:C	(self)
ss13872783	NT_016354.16:3535683:T:C	NC_000004.12:78119824:T:C	(self)
ss66539195, ss66865100, ss66935596, ss68421994, ss70356550, ss70460472, ss70981164, ss75326920, ss84891996, ss98973569, ss121254302, ss143781812, ss152545437, ss159104384, ss169217742, ss169531092	NT_016354.19:3588699:T:C	NC_000004.12:78119824:T:C	(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 rs10025977

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

rs10025977