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dbSNP Short Genetic Variations

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.

rs41299046

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr9:134750643 (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
G>A / G>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.089992 (23820/264690, TOPMED)
C=0.073370 (18384/250564, GnomAD_exome)
C=0.092210 (12929/140212, GnomAD) (+ 18 more)
C=0.076781 (9238/120316, ExAC)
C=0.08293 (2318/27952, ALFA)
C=0.09772 (1271/13006, GO-ESP)
C=0.0779 (499/6404, 1000G_30x)
C=0.0765 (383/5008, 1000G)
C=0.0795 (356/4480, Estonian)
C=0.0973 (375/3854, ALSPAC)
C=0.0998 (370/3708, TWINSUK)
C=0.0011 (2/1832, Korea1K)
C=0.084 (84/998, GoNL)
C=0.075 (45/600, NorthernSweden)
C=0.054 (29/534, MGP)
C=0.076 (23/304, FINRISK)
C=0.060 (13/216, Qatari)
G=0.47 (31/66, SGDP_PRJ)
C=0.10 (4/40, GENOME_DK)
G=0.5 (2/4, Siberian)
C=0.5 (2/4, Siberian)
Clinical Significance
Reported in ClinVar
Gene : Consequence
COL5A1 : 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 27952 G=0.91707 C=0.08293
European Sub 20398 G=0.91906 C=0.08094
African Sub 3554 G=0.8849 C=0.1151
African Others Sub 122 G=0.861 C=0.139
African American Sub 3432 G=0.8858 C=0.1142
Asian Sub 168 G=0.994 C=0.006
East Asian Sub 112 G=1.000 C=0.000
Other Asian Sub 56 G=0.98 C=0.02
Latin American 1 Sub 146 G=0.932 C=0.068
Latin American 2 Sub 610 G=0.954 C=0.046
South Asian Sub 98 G=0.92 C=0.08
Other Sub 2978 G=0.9291 C=0.0709


Help

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 G=0.910008 C=0.089992
gnomAD - Exomes Global Study-wide 250564 G=0.926630 C=0.073370
gnomAD - Exomes European Sub 134664 G=0.910013 C=0.089987
gnomAD - Exomes Asian Sub 49000 G=0.95806 C=0.04194
gnomAD - Exomes American Sub 34572 G=0.95913 C=0.04087
gnomAD - Exomes African Sub 16166 G=0.87672 C=0.12328
gnomAD - Exomes Ashkenazi Jewish Sub 10042 G=0.96126 C=0.03874
gnomAD - Exomes Other Sub 6120 G=0.9320 C=0.0680
gnomAD - Genomes Global Study-wide 140212 G=0.907790 C=0.092210
gnomAD - Genomes European Sub 75924 G=0.91098 C=0.08902
gnomAD - Genomes African Sub 42020 G=0.87937 C=0.12063
gnomAD - Genomes American Sub 13656 G=0.94339 C=0.05661
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=0.9564 C=0.0436
gnomAD - Genomes East Asian Sub 3134 G=0.9981 C=0.0019
gnomAD - Genomes Other Sub 2154 G=0.9178 C=0.0822
ExAC Global Study-wide 120316 G=0.923219 C=0.076781
ExAC Europe Sub 72432 G=0.91190 C=0.08810
ExAC Asian Sub 25148 G=0.95586 C=0.04414
ExAC American Sub 11548 G=0.96285 C=0.03715
ExAC African Sub 10288 G=0.87860 C=0.12140
ExAC Other Sub 900 G=0.923 C=0.077
Allele Frequency Aggregator Total Global 27952 G=0.91707 C=0.08293
Allele Frequency Aggregator European Sub 20398 G=0.91906 C=0.08094
Allele Frequency Aggregator African Sub 3554 G=0.8849 C=0.1151
Allele Frequency Aggregator Other Sub 2978 G=0.9291 C=0.0709
Allele Frequency Aggregator Latin American 2 Sub 610 G=0.954 C=0.046
Allele Frequency Aggregator Asian Sub 168 G=0.994 C=0.006
Allele Frequency Aggregator Latin American 1 Sub 146 G=0.932 C=0.068
Allele Frequency Aggregator South Asian Sub 98 G=0.92 C=0.08
GO Exome Sequencing Project Global Study-wide 13006 G=0.90228 C=0.09772
GO Exome Sequencing Project European American Sub 8600 G=0.9129 C=0.0871
GO Exome Sequencing Project African American Sub 4406 G=0.8815 C=0.1185
1000Genomes_30x Global Study-wide 6404 G=0.9221 C=0.0779
1000Genomes_30x African Sub 1786 G=0.8634 C=0.1366
1000Genomes_30x Europe Sub 1266 G=0.9123 C=0.0877
1000Genomes_30x South Asian Sub 1202 G=0.9359 C=0.0641
1000Genomes_30x East Asian Sub 1170 G=0.9983 C=0.0017
1000Genomes_30x American Sub 980 G=0.934 C=0.066
1000Genomes Global Study-wide 5008 G=0.9235 C=0.0765
1000Genomes African Sub 1322 G=0.8563 C=0.1437
1000Genomes East Asian Sub 1008 G=0.9980 C=0.0020
1000Genomes Europe Sub 1006 G=0.9155 C=0.0845
1000Genomes South Asian Sub 978 G=0.936 C=0.064
1000Genomes American Sub 694 G=0.938 C=0.062
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.9205 C=0.0795
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.9027 C=0.0973
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.9002 C=0.0998
Korean Genome Project KOREAN Study-wide 1832 G=0.9989 C=0.0011
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.916 C=0.084
Northern Sweden ACPOP Study-wide 600 G=0.925 C=0.075
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 G=0.946 C=0.054
FINRISK Finnish from FINRISK project Study-wide 304 G=0.924 C=0.076
Qatari Global Study-wide 216 G=0.940 C=0.060
SGDP_PRJ Global Study-wide 66 G=0.47 C=0.53
The Danish reference pan genome Danish Study-wide 40 G=0.90 C=0.10
Siberian Global Study-wide 4 G=0.5 C=0.5
Help

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.134750643G>A
GRCh38.p14 chr 9 NC_000009.12:g.134750643G>C
GRCh37.p13 chr 9 NC_000009.11:g.137642489G>A
GRCh37.p13 chr 9 NC_000009.11:g.137642489G>C
COL5A1 RefSeqGene (LRG_737) NG_008030.1:g.113838G>A
COL5A1 RefSeqGene (LRG_737) NG_008030.1:g.113838G>C
Gene: COL5A1, collagen type V alpha 1 chain (plus strand)
Molecule type Change Amino acid[Codon] SO Term
COL5A1 transcript variant 1 NM_000093.5:c.1569+27G>A N/A Intron Variant
COL5A1 transcript variant 2 NM_001278074.1:c.1569+27G…

NM_001278074.1:c.1569+27G>A

N/A Intron Variant
COL5A1 transcript variant X1 XM_017014266.3:c.1569+27G…

XM_017014266.3:c.1569+27G>A

N/A Intron Variant
Help

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: C (allele ID: 1266854 )
ClinVar Accession Disease Names Clinical Significance
RCV001690290.1 not provided Benign
Help

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 G= A C
GRCh38.p14 chr 9 NC_000009.12:g.134750643= NC_000009.12:g.134750643G>A NC_000009.12:g.134750643G>C
GRCh37.p13 chr 9 NC_000009.11:g.137642489= NC_000009.11:g.137642489G>A NC_000009.11:g.137642489G>C
COL5A1 RefSeqGene (LRG_737) NG_008030.1:g.113838= NG_008030.1:g.113838G>A NG_008030.1:g.113838G>C
COL5A1 transcript variant 1 NM_000093.4:c.1569+27= NM_000093.4:c.1569+27G>A NM_000093.4:c.1569+27G>C
COL5A1 transcript variant 1 NM_000093.5:c.1569+27= NM_000093.5:c.1569+27G>A NM_000093.5:c.1569+27G>C
COL5A1 transcript variant 2 NM_001278074.1:c.1569+27= NM_001278074.1:c.1569+27G>A NM_001278074.1:c.1569+27G>C
COL5A1 transcript variant X1 XM_017014266.3:c.1569+27= XM_017014266.3:c.1569+27G>A XM_017014266.3:c.1569+27G>C
Help

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, 24 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 SI_EXO ss61705007 Oct 18, 2006 (127)
2 1000GENOMES ss115179972 Jan 25, 2009 (130)
3 COMPLETE_GENOMICS ss165894168 Jul 04, 2010 (132)
4 BUSHMAN ss200985377 Jul 04, 2010 (132)
5 1000GENOMES ss224497075 Jul 14, 2010 (132)
6 1000GENOMES ss235001714 Jul 15, 2010 (132)
7 BL ss254623999 May 09, 2011 (134)
8 1000GENOMES ss490989104 May 04, 2012 (137)
9 ILLUMINA ss536070721 Sep 08, 2015 (146)
10 TISHKOFF ss561689231 Apr 25, 2013 (138)
11 SSMP ss656185626 Apr 25, 2013 (138)
12 NHLBI-ESP ss712927539 Apr 25, 2013 (138)
13 EVA-GONL ss987066159 Aug 21, 2014 (142)
14 JMKIDD_LAB ss1076669208 Aug 21, 2014 (142)
15 1000GENOMES ss1335788627 Aug 21, 2014 (142)
16 DDI ss1431984822 Apr 01, 2015 (144)
17 EVA_GENOME_DK ss1583290486 Apr 01, 2015 (144)
18 EVA_FINRISK ss1584065654 Apr 01, 2015 (144)
19 EVA_DECODE ss1596713493 Apr 01, 2015 (144)
20 EVA_UK10K_ALSPAC ss1623739376 Apr 01, 2015 (144)
21 EVA_UK10K_TWINSUK ss1666733409 Apr 01, 2015 (144)
22 EVA_EXAC ss1689732302 Apr 01, 2015 (144)
23 EVA_MGP ss1711242168 Apr 01, 2015 (144)
24 WEILL_CORNELL_DGM ss1930381166 Feb 12, 2016 (147)
25 JJLAB ss2025914044 Sep 14, 2016 (149)
26 USC_VALOUEV ss2154150461 Dec 20, 2016 (150)
27 HUMAN_LONGEVITY ss2315125726 Dec 20, 2016 (150)
28 GNOMAD ss2737986369 Nov 08, 2017 (151)
29 GNOMAD ss2748303965 Nov 08, 2017 (151)
30 GNOMAD ss2884159090 Nov 08, 2017 (151)
31 SWEGEN ss3005730237 Nov 08, 2017 (151)
32 BIOINF_KMB_FNS_UNIBA ss3026739369 Nov 08, 2017 (151)
33 CSHL ss3348896097 Nov 08, 2017 (151)
34 ILLUMINA ss3630377440 Oct 12, 2018 (152)
35 OMUKHERJEE_ADBS ss3646399960 Oct 12, 2018 (152)
36 EGCUT_WGS ss3673267447 Jul 13, 2019 (153)
37 EVA_DECODE ss3724925154 Jul 13, 2019 (153)
38 ACPOP ss3736948254 Jul 13, 2019 (153)
39 EVA ss3769795091 Jul 13, 2019 (153)
40 KHV_HUMAN_GENOMES ss3812955930 Jul 13, 2019 (153)
41 EVA ss3824482338 Apr 26, 2020 (154)
42 EVA ss3831902106 Apr 26, 2020 (154)
43 SGDP_PRJ ss3873250001 Apr 26, 2020 (154)
44 KOGIC ss3966944700 Apr 26, 2020 (154)
45 FSA-LAB ss3984434182 Apr 26, 2021 (155)
46 EVA ss3986468213 Apr 26, 2021 (155)
47 TOPMED ss4838513413 Apr 26, 2021 (155)
48 TOMMO_GENOMICS ss5195692951 Apr 26, 2021 (155)
49 TOMMO_GENOMICS ss5195692952 Apr 26, 2021 (155)
50 1000G_HIGH_COVERAGE ss5282479055 Oct 16, 2022 (156)
51 EVA ss5390804808 Oct 16, 2022 (156)
52 HUGCELL_USP ss5478313792 Oct 16, 2022 (156)
53 EVA ss5509870796 Oct 16, 2022 (156)
54 1000G_HIGH_COVERAGE ss5575675849 Oct 16, 2022 (156)
55 SANFORD_IMAGENETICS ss5648428299 Oct 16, 2022 (156)
56 TOMMO_GENOMICS ss5740358999 Oct 16, 2022 (156)
57 TOMMO_GENOMICS ss5740359000 Oct 16, 2022 (156)
58 YY_MCH ss5811079794 Oct 16, 2022 (156)
59 EVA ss5829866216 Oct 16, 2022 (156)
60 EVA ss5848734683 Oct 16, 2022 (156)
61 EVA ss5918365963 Oct 16, 2022 (156)
62 EVA ss5977642726 Oct 16, 2022 (156)
63 1000Genomes NC_000009.11 - 137642489 Oct 12, 2018 (152)
64 1000Genomes_30x NC_000009.12 - 134750643 Oct 16, 2022 (156)
65 The Avon Longitudinal Study of Parents and Children NC_000009.11 - 137642489 Oct 12, 2018 (152)
66 Genetic variation in the Estonian population NC_000009.11 - 137642489 Oct 12, 2018 (152)
67 ExAC NC_000009.11 - 137642489 Oct 12, 2018 (152)
68 FINRISK NC_000009.11 - 137642489 Apr 26, 2020 (154)
69 The Danish reference pan genome NC_000009.11 - 137642489 Apr 26, 2020 (154)
70 gnomAD - Genomes NC_000009.12 - 134750643 Apr 26, 2021 (155)
71 gnomAD - Exomes NC_000009.11 - 137642489 Jul 13, 2019 (153)
72 GO Exome Sequencing Project NC_000009.11 - 137642489 Oct 12, 2018 (152)
73 Genome of the Netherlands Release 5 NC_000009.11 - 137642489 Apr 26, 2020 (154)
74 Korean Genome Project NC_000009.12 - 134750643 Apr 26, 2020 (154)
75 Medical Genome Project healthy controls from Spanish population NC_000009.11 - 137642489 Apr 26, 2020 (154)
76 Northern Sweden NC_000009.11 - 137642489 Jul 13, 2019 (153)
77 Qatari NC_000009.11 - 137642489 Apr 26, 2020 (154)
78 SGDP_PRJ NC_000009.11 - 137642489 Apr 26, 2020 (154)
79 Siberian NC_000009.11 - 137642489 Apr 26, 2020 (154)
80 8.3KJPN

Submission ignored due to conflicting rows:
Row 53662258 (NC_000009.11:137642488:G:C 2/16760)
Row 53662259 (NC_000009.11:137642488:G:A 1/16760)

- Apr 26, 2021 (155)
81 8.3KJPN

Submission ignored due to conflicting rows:
Row 53662258 (NC_000009.11:137642488:G:C 2/16760)
Row 53662259 (NC_000009.11:137642488:G:A 1/16760)

- Apr 26, 2021 (155)
82 14KJPN

Submission ignored due to conflicting rows:
Row 74196103 (NC_000009.12:134750642:G:C 2/28258)
Row 74196104 (NC_000009.12:134750642:G:A 1/28258)

- Oct 16, 2022 (156)
83 14KJPN

Submission ignored due to conflicting rows:
Row 74196103 (NC_000009.12:134750642:G:C 2/28258)
Row 74196104 (NC_000009.12:134750642:G:A 1/28258)

- Oct 16, 2022 (156)
84 TopMed NC_000009.12 - 134750643 Apr 26, 2021 (155)
85 UK 10K study - Twins NC_000009.11 - 137642489 Oct 12, 2018 (152)
86 ALFA NC_000009.12 - 134750643 Apr 26, 2021 (155)
87 ClinVar RCV001690290.1 Oct 16, 2022 (156)
Help

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
ss5195692952 NC_000009.11:137642488:G:A NC_000009.12:134750642:G:A (self)
ss5740359000 NC_000009.12:134750642:G:A NC_000009.12:134750642:G:A
ss115179972, ss165894168, ss200985377, ss254623999, ss1596713493 NC_000009.10:136782309:G:C NC_000009.12:134750642:G:C (self)
48118517, 26743040, 19005695, 9873538, 62115, 9455423, 7176980, 940073, 11927263, 357928, 10233119, 12423096, 25266981, 6666815, 26743040, ss224497075, ss235001714, ss490989104, ss536070721, ss561689231, ss656185626, ss712927539, ss987066159, ss1076669208, ss1335788627, ss1431984822, ss1583290486, ss1584065654, ss1623739376, ss1666733409, ss1689732302, ss1711242168, ss1930381166, ss2025914044, ss2154150461, ss2737986369, ss2748303965, ss2884159090, ss3005730237, ss3348896097, ss3630377440, ss3646399960, ss3673267447, ss3736948254, ss3769795091, ss3824482338, ss3831902106, ss3873250001, ss3984434182, ss3986468213, ss5195692951, ss5390804808, ss5509870796, ss5648428299, ss5829866216, ss5848734683, ss5977642726 NC_000009.11:137642488:G:C NC_000009.12:134750642:G:C (self)
RCV001690290.1, 63201784, 340054691, 23322701, 675890974, 12675173792, ss2315125726, ss3026739369, ss3724925154, ss3812955930, ss3966944700, ss4838513413, ss5282479055, ss5478313792, ss5575675849, ss5740358999, ss5811079794, ss5918365963 NC_000009.12:134750642:G:C NC_000009.12:134750642:G:C (self)
ss61705007 NT_019501.12:357953:G:C NC_000009.12:134750642:G:C (self)
Help

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

No publications for rs41299046

Help

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.

Software version is: 2.0.1.post761+d5e8e07