Name: rs41308900
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.

rs41308900

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr9:99035048 (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=0.015086 (3993/264690, TOPMED)
T=0.015849 (3925/247656, GnomAD_exome)
T=0.022109 (3690/166900, ALFA) (+ 14 more)
T=0.015624 (2191/140236, GnomAD)
T=0.015876 (1879/118358, ExAC)
T=0.00703 (553/78636, PAGE_STUDY)
T=0.01507 (196/13006, GO-ESP)
T=0.0072 (46/6404, 1000G_30x)
T=0.0068 (34/5008, 1000G)
T=0.0094 (42/4480, Estonian)
T=0.0234 (90/3854, ALSPAC)
T=0.0232 (86/3708, TWINSUK)
T=0.024 (24/998, GoNL)
T=0.027 (16/600, NorthernSweden)
T=0.011 (6/534, MGP)
T=0.023 (7/304, FINRISK)
T=0.014 (3/216, Qatari)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: COL15A1 : Missense Variant
Publications: 1 citation
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	183016	C=0.978406	T=0.021594
European	Sub	147842	C=0.976069	T=0.023931
African	Sub	9966	C=0.9946	T=0.0054
African Others	Sub	356	C=1.000	T=0.000
African American	Sub	9610	C=0.9944	T=0.0056
Asian	Sub	6346	C=1.0000	T=0.0000
East Asian	Sub	4498	C=1.0000	T=0.0000
Other Asian	Sub	1848	C=1.0000	T=0.0000
Latin American 1	Sub	810	C=0.994	T=0.006
Latin American 2	Sub	1000	C=0.992	T=0.008
South Asian	Sub	296	C=1.000	T=0.000
Other	Sub	16756	C=0.97929	T=0.02071

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=0.984914	T=0.015086
gnomAD - Exomes	Global	Study-wide	247656	C=0.984151	T=0.015849
gnomAD - Exomes	European	Sub	132126	C=0.978619	T=0.021381
gnomAD - Exomes	Asian	Sub	48940	C=0.99647	T=0.00353
gnomAD - Exomes	American	Sub	34542	C=0.99244	T=0.00756
gnomAD - Exomes	African	Sub	15946	C=0.99668	T=0.00332
gnomAD - Exomes	Ashkenazi Jewish	Sub	10008	C=0.94954	T=0.05046
gnomAD - Exomes	Other	Sub	6094	C=0.9823	T=0.0177
Allele Frequency Aggregator	Total	Global	166900	C=0.977891	T=0.022109
Allele Frequency Aggregator	European	Sub	137926	C=0.975951	T=0.024049
Allele Frequency Aggregator	Other	Sub	15332	C=0.97854	T=0.02146
Allele Frequency Aggregator	Asian	Sub	6346	C=1.0000	T=0.0000
Allele Frequency Aggregator	African	Sub	5190	C=0.9940	T=0.0060
Allele Frequency Aggregator	Latin American 2	Sub	1000	C=0.992	T=0.008
Allele Frequency Aggregator	Latin American 1	Sub	810	C=0.994	T=0.006
Allele Frequency Aggregator	South Asian	Sub	296	C=1.000	T=0.000
gnomAD - Genomes	Global	Study-wide	140236	C=0.984376	T=0.015624
gnomAD - Genomes	European	Sub	75928	C=0.97811	T=0.02189
gnomAD - Genomes	African	Sub	42040	C=0.99586	T=0.00414
gnomAD - Genomes	American	Sub	13662	C=0.98858	T=0.01142
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	C=0.9501	T=0.0499
gnomAD - Genomes	East Asian	Sub	3132	C=0.9997	T=0.0003
gnomAD - Genomes	Other	Sub	2150	C=0.9851	T=0.0149
ExAC	Global	Study-wide	118358	C=0.984124	T=0.015876
ExAC	Europe	Sub	71300	C=0.97675	T=0.02325
ExAC	Asian	Sub	24976	C=0.99628	T=0.00372
ExAC	American	Sub	11498	C=0.99304	T=0.00696
ExAC	African	Sub	9696	C=0.9964	T=0.0036
ExAC	Other	Sub	888	C=0.985	T=0.015
The PAGE Study	Global	Study-wide	78636	C=0.99297	T=0.00703
The PAGE Study	AfricanAmerican	Sub	32472	C=0.99440	T=0.00560
The PAGE Study	Mexican	Sub	10802	C=0.98982	T=0.01018
The PAGE Study	Asian	Sub	8314	C=0.9996	T=0.0004
The PAGE Study	PuertoRican	Sub	7918	C=0.9888	T=0.0112
The PAGE Study	NativeHawaiian	Sub	4530	C=0.9927	T=0.0073
The PAGE Study	Cuban	Sub	4226	C=0.9877	T=0.0123
The PAGE Study	Dominican	Sub	3828	C=0.9932	T=0.0068
The PAGE Study	CentralAmerican	Sub	2448	C=0.9914	T=0.0086
The PAGE Study	SouthAmerican	Sub	1982	C=0.9914	T=0.0086
The PAGE Study	NativeAmerican	Sub	1260	C=0.9857	T=0.0143
The PAGE Study	SouthAsian	Sub	856	C=0.998	T=0.002
GO Exome Sequencing Project	Global	Study-wide	13006	C=0.98493	T=0.01507
GO Exome Sequencing Project	European American	Sub	8600	C=0.9790	T=0.0210
GO Exome Sequencing Project	African American	Sub	4406	C=0.9966	T=0.0034
1000Genomes_30x	Global	Study-wide	6404	C=0.9928	T=0.0072
1000Genomes_30x	African	Sub	1786	C=1.0000	T=0.0000
1000Genomes_30x	Europe	Sub	1266	C=0.9810	T=0.0190
1000Genomes_30x	South Asian	Sub	1202	C=0.9958	T=0.0042
1000Genomes_30x	East Asian	Sub	1170	C=1.0000	T=0.0000
1000Genomes_30x	American	Sub	980	C=0.983	T=0.017
1000Genomes	Global	Study-wide	5008	C=0.9932	T=0.0068
1000Genomes	African	Sub	1322	C=1.0000	T=0.0000
1000Genomes	East Asian	Sub	1008	C=1.0000	T=0.0000
1000Genomes	Europe	Sub	1006	C=0.9831	T=0.0169
1000Genomes	South Asian	Sub	978	C=0.995	T=0.005
1000Genomes	American	Sub	694	C=0.983	T=0.017
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.9906	T=0.0094
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.9766	T=0.0234
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.9768	T=0.0232
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.976	T=0.024
Northern Sweden	ACPOP	Study-wide	600	C=0.973	T=0.027
Medical Genome Project healthy controls from Spanish population	Spanish controls	Study-wide	534	C=0.989	T=0.011
FINRISK	Finnish from FINRISK project	Study-wide	304	C=0.977	T=0.023
Qatari	Global	Study-wide	216	C=0.986	T=0.014

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 9	NC_000009.12:g.99035048C>T
GRCh37.p13 chr 9	NC_000009.11:g.101797330C>T

Gene: COL15A1, collagen type XV alpha 1 chain (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
COL15A1 transcript	NM_001855.5:c.2114C>T	P [CCG] > L [CTG]	Coding Sequence Variant
collagen alpha-1(XV) chain precursor	NP_001846.3:p.Pro705Leu	P (Pro) > L (Leu)	Missense Variant
COL15A1 transcript variant X1	XM_047422759.1:c.2114C>T	P [CCG] > L [CTG]	Coding Sequence Variant
collagen alpha-1(XV) chain isoform X1	XP_047278715.1:p.Pro705Leu	P (Pro) > L (Leu)	Missense Variant
COL15A1 transcript variant X2	XM_011518214.3:c.2114C>T	P [CCG] > L [CTG]	Coding Sequence Variant
collagen alpha-1(XV) chain isoform X1	XP_011516516.1:p.Pro705Leu	P (Pro) > L (Leu)	Missense Variant
COL15A1 transcript variant X3	XM_047422760.1:c.2114C>T	P [CCG] > L [CTG]	Coding Sequence Variant
collagen alpha-1(XV) chain isoform X1	XP_047278716.1:p.Pro705Leu	P (Pro) > L (Leu)	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 9	NC_000009.12:g.99035048=	NC_000009.12:g.99035048C>T
GRCh37.p13 chr 9	NC_000009.11:g.101797330=	NC_000009.11:g.101797330C>T
COL15A1 transcript	NM_001855.5:c.2114=	NM_001855.5:c.2114C>T
COL15A1 transcript	NM_001855.4:c.2114=	NM_001855.4:c.2114C>T
COL15A1 transcript variant X2	XM_011518214.3:c.2114=	XM_011518214.3:c.2114C>T
COL15A1 transcript variant X1	XM_011518214.2:c.2114=	XM_011518214.2:c.2114C>T
COL15A1 transcript variant X1	XM_011518214.1:c.2114=	XM_011518214.1:c.2114C>T
COL15A1 transcript variant X1	XM_047422759.1:c.2114=	XM_047422759.1:c.2114C>T
COL15A1 transcript variant X3	XM_047422760.1:c.2114=	XM_047422760.1:c.2114C>T
collagen alpha-1(XV) chain precursor	NP_001846.3:p.Pro705=	NP_001846.3:p.Pro705Leu
collagen alpha-1(XV) chain isoform X1	XP_011516516.1:p.Pro705=	XP_011516516.1:p.Pro705Leu
collagen alpha-1(XV) chain isoform X1	XP_047278715.1:p.Pro705=	XP_047278715.1:p.Pro705Leu
collagen alpha-1(XV) chain isoform X1	XP_047278716.1:p.Pro705=	XP_047278716.1:p.Pro705Leu

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#.

67 SubSNP, 17 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SI_EXO	ss61716674	Oct 18, 2006 (127)
2	BCMHGSC_JDW	ss94112684	Mar 25, 2008 (130)
3	1000GENOMES	ss108938281	Jan 23, 2009 (130)
4	ENSEMBL	ss144275551	Dec 01, 2009 (131)
5	SEATTLESEQ	ss159718714	Dec 01, 2009 (131)
6	ILLUMINA	ss161104458	Dec 01, 2009 (131)
7	1000GENOMES	ss234900854	Jul 15, 2010 (132)
8	NHLBI-ESP	ss342278484	May 09, 2011 (134)
9	ILLUMINA	ss479424004	Sep 08, 2015 (146)
10	1000GENOMES	ss490981491	May 04, 2012 (137)
11	EXOME_CHIP	ss491425341	May 04, 2012 (137)
12	CLINSEQ_SNP	ss491939796	May 04, 2012 (137)
13	EVA-GONL	ss986793526	Aug 21, 2014 (142)
14	1000GENOMES	ss1334758843	Aug 21, 2014 (142)
15	EVA_FINRISK	ss1584063399	Apr 01, 2015 (144)
16	EVA_DECODE	ss1596429508	Apr 01, 2015 (144)
17	EVA_UK10K_ALSPAC	ss1623187464	Apr 01, 2015 (144)
18	EVA_UK10K_TWINSUK	ss1666181497	Apr 01, 2015 (144)
19	EVA_EXAC	ss1689577592	Apr 01, 2015 (144)
20	EVA_MGP	ss1711231297	Apr 01, 2015 (144)
21	ILLUMINA	ss1917838503	Feb 12, 2016 (147)
22	WEILL_CORNELL_DGM	ss1930108269	Feb 12, 2016 (147)
23	ILLUMINA	ss1959200387	Feb 12, 2016 (147)
24	JJLAB	ss2025772601	Sep 14, 2016 (149)
25	HUMAN_LONGEVITY	ss2312982714	Dec 20, 2016 (150)
26	GNOMAD	ss2737749442	Nov 08, 2017 (151)
27	GNOMAD	ss2748231067	Nov 08, 2017 (151)
28	GNOMAD	ss2881243213	Nov 08, 2017 (151)
29	AFFY	ss2985467905	Nov 08, 2017 (151)
30	SWEGEN	ss3005307689	Nov 08, 2017 (151)
31	ILLUMINA	ss3022947664	Nov 08, 2017 (151)
32	CSHL	ss3348776750	Nov 08, 2017 (151)
33	ILLUMINA	ss3635223689	Oct 12, 2018 (152)
34	ILLUMINA	ss3636972037	Oct 12, 2018 (152)
35	ILLUMINA	ss3640930980	Oct 12, 2018 (152)
36	ILLUMINA	ss3644997111	Oct 12, 2018 (152)
37	ILLUMINA	ss3653501165	Oct 12, 2018 (152)
38	ILLUMINA	ss3654232725	Oct 12, 2018 (152)
39	EGCUT_WGS	ss3672841871	Jul 13, 2019 (153)
40	EVA_DECODE	ss3724408166	Jul 13, 2019 (153)
41	ILLUMINA	ss3726627990	Jul 13, 2019 (153)
42	ACPOP	ss3736721669	Jul 13, 2019 (153)
43	ILLUMINA	ss3744591206	Jul 13, 2019 (153)
44	ILLUMINA	ss3745523609	Jul 13, 2019 (153)
45	PAGE_CC	ss3771513174	Jul 13, 2019 (153)
46	KHV_HUMAN_GENOMES	ss3812639521	Jul 13, 2019 (153)
47	EVA	ss3824448017	Apr 26, 2020 (154)
48	EVA	ss3825758910	Apr 26, 2020 (154)
49	EVA	ss3839412618	Apr 26, 2020 (154)
50	EVA	ss3844876516	Apr 26, 2020 (154)
51	FSA-LAB	ss3984423996	Apr 26, 2021 (155)
52	FSA-LAB	ss3984423997	Apr 26, 2021 (155)
53	EVA	ss3986454853	Apr 26, 2021 (155)
54	TOPMED	ss4829514112	Apr 26, 2021 (155)
55	1000G_HIGH_COVERAGE	ss5281570933	Oct 13, 2022 (156)
56	EVA	ss5389135255	Oct 13, 2022 (156)
57	HUGCELL_USP	ss5477495924	Oct 13, 2022 (156)
58	1000G_HIGH_COVERAGE	ss5574322600	Oct 13, 2022 (156)
59	SANFORD_IMAGENETICS	ss5624725337	Oct 13, 2022 (156)
60	SANFORD_IMAGENETICS	ss5647920768	Oct 13, 2022 (156)
61	EVA	ss5829507436	Oct 13, 2022 (156)
62	EVA	ss5847359947	Oct 13, 2022 (156)
63	EVA	ss5848212929	Oct 13, 2022 (156)
64	EVA	ss5848726335	Oct 13, 2022 (156)
65	EVA	ss5917321374	Oct 13, 2022 (156)
66	EVA	ss5977110992	Oct 13, 2022 (156)
67	EVA	ss5979900211	Oct 13, 2022 (156)
68	1000Genomes	NC_000009.11 - 101797330	Oct 12, 2018 (152)
69	1000Genomes_30x	NC_000009.12 - 99035048	Oct 13, 2022 (156)
70	The Avon Longitudinal Study of Parents and Children	NC_000009.11 - 101797330	Oct 12, 2018 (152)
71	Genetic variation in the Estonian population	NC_000009.11 - 101797330	Oct 12, 2018 (152)
72	ExAC	NC_000009.11 - 101797330	Oct 12, 2018 (152)
73	FINRISK	NC_000009.11 - 101797330	Apr 26, 2020 (154)
74	gnomAD - Genomes	NC_000009.12 - 99035048	Apr 26, 2021 (155)
75	gnomAD - Exomes	NC_000009.11 - 101797330	Jul 13, 2019 (153)
76	GO Exome Sequencing Project	NC_000009.11 - 101797330	Oct 12, 2018 (152)
77	Genome of the Netherlands Release 5	NC_000009.11 - 101797330	Apr 26, 2020 (154)
78	Medical Genome Project healthy controls from Spanish population	NC_000009.11 - 101797330	Apr 26, 2020 (154)
79	Northern Sweden	NC_000009.11 - 101797330	Jul 13, 2019 (153)
80	The PAGE Study	NC_000009.12 - 99035048	Jul 13, 2019 (153)
81	Qatari	NC_000009.11 - 101797330	Apr 26, 2020 (154)
82	TopMed	NC_000009.12 - 99035048	Apr 26, 2021 (155)
83	UK 10K study - Twins	NC_000009.11 - 101797330	Oct 12, 2018 (152)
84	ALFA	NC_000009.12 - 99035048	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)
rs62561257	May 26, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss94112684, ss108938281, ss491939796, ss1596429508	NC_000009.10:100837150:C:T	NC_000009.12:99035047:C:T	(self)
47051544, 26136151, 18580119, 9707979, 59860, 6934218, 905791, 11663644, 347057, 10006534, 12150199, 26136151, ss234900854, ss342278484, ss479424004, ss490981491, ss491425341, ss986793526, ss1334758843, ss1584063399, ss1623187464, ss1666181497, ss1689577592, ss1711231297, ss1917838503, ss1930108269, ss1959200387, ss2025772601, ss2737749442, ss2748231067, ss2881243213, ss2985467905, ss3005307689, ss3022947664, ss3348776750, ss3635223689, ss3636972037, ss3640930980, ss3644997111, ss3653501165, ss3654232725, ss3672841871, ss3736721669, ss3744591206, ss3745523609, ss3824448017, ss3825758910, ss3839412618, ss3984423996, ss3984423997, ss3986454853, ss5389135255, ss5624725337, ss5647920768, ss5829507436, ss5847359947, ss5848212929, ss5848726335, ss5977110992, ss5979900211	NC_000009.11:101797329:C:T	NC_000009.12:99035047:C:T	(self)
61848535, 332628295, 734643, 666891673, 150963891, ss2312982714, ss3724408166, ss3726627990, ss3771513174, ss3812639521, ss3844876516, ss4829514112, ss5281570933, ss5477495924, ss5574322600, ss5917321374	NC_000009.12:99035047:C:T	NC_000009.12:99035047:C:T	(self)
ss61716674	NT_008470.17:9118534:C:T	NC_000009.12:99035047:C:T	(self)
ss144275551, ss159718714, ss161104458	NT_008470.19:30961861:C:T	NC_000009.12:99035047:C:T	(self)

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

1 citation for rs41308900

PMID	Title	Author	Year	Journal
27007659	Whole Exome Sequencing in Patients with the Cuticular Drusen Subtype of Age-Related Macular Degeneration.	Duvvari MR et al.	2016	PloS one

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

rs41308900