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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.

rs150124840

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr7:94428379 (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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000207 (52/251256, GnomAD_exome)
T=0.000077 (13/168904, ALFA)
T=0.000542 (76/140150, GnomAD) (+ 9 more)
T=0.000297 (36/121380, ExAC)
T=0.00085 (67/78702, PAGE_STUDY)
T=0.00100 (13/13006, GO-ESP)
T=0.0009 (6/6404, 1000G_30x)
T=0.0006 (3/5008, 1000G)
T=0.0000 (0/3854, ALSPAC)
T=0.0003 (1/3708, TWINSUK)
C=0.5 (1/2, SGDP_PRJ)
T=0.5 (1/2, SGDP_PRJ)
Clinical Significance
Reported in ClinVar
Gene : Consequence
COL1A2 : 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 185308 C=0.999887 A=0.000000, T=0.000113
European Sub 157120 C=0.999968 A=0.000000, T=0.000032
African Sub 9164 C=0.9987 A=0.0000, T=0.0013
African Others Sub 352 C=0.997 A=0.000, T=0.003
African American Sub 8812 C=0.9988 A=0.0000, T=0.0012
Asian Sub 6294 C=1.0000 A=0.0000, T=0.0000
East Asian Sub 4476 C=1.0000 A=0.0000, T=0.0000
Other Asian Sub 1818 C=1.0000 A=0.0000, T=0.0000
Latin American 1 Sub 442 C=0.995 A=0.000, T=0.005
Latin American 2 Sub 950 C=0.999 A=0.000, T=0.001
South Asian Sub 280 C=1.000 A=0.000, T=0.000
Other Sub 11058 C=0.99991 A=0.00000, T=0.00009


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
gnomAD - Exomes Global Study-wide 251256 C=0.999793 T=0.000207
gnomAD - Exomes European Sub 135208 C=0.999963 T=0.000037
gnomAD - Exomes Asian Sub 49004 C=1.00000 T=0.00000
gnomAD - Exomes American Sub 34588 C=0.99983 T=0.00017
gnomAD - Exomes African Sub 16256 C=0.99766 T=0.00234
gnomAD - Exomes Ashkenazi Jewish Sub 10068 C=1.00000 T=0.00000
gnomAD - Exomes Other Sub 6132 C=0.9995 T=0.0005
Allele Frequency Aggregator Total Global 168904 C=0.999923 A=0.000000, T=0.000077
Allele Frequency Aggregator European Sub 146986 C=0.999966 A=0.000000, T=0.000034
Allele Frequency Aggregator Other Sub 9626 C=0.9999 A=0.0000, T=0.0001
Allele Frequency Aggregator Asian Sub 6294 C=1.0000 A=0.0000, T=0.0000
Allele Frequency Aggregator African Sub 4326 C=0.9991 A=0.0000, T=0.0009
Allele Frequency Aggregator Latin American 2 Sub 950 C=0.999 A=0.000, T=0.001
Allele Frequency Aggregator Latin American 1 Sub 442 C=0.995 A=0.000, T=0.005
Allele Frequency Aggregator South Asian Sub 280 C=1.000 A=0.000, T=0.000
gnomAD - Genomes Global Study-wide 140150 C=0.999458 T=0.000542
gnomAD - Genomes European Sub 75914 C=0.99996 T=0.00004
gnomAD - Genomes African Sub 41992 C=0.99831 T=0.00169
gnomAD - Genomes American Sub 13644 C=1.00000 T=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3322 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3130 C=0.9997 T=0.0003
gnomAD - Genomes Other Sub 2148 C=0.9995 T=0.0005
ExAC Global Study-wide 121380 C=0.999703 T=0.000297
ExAC Europe Sub 73340 C=0.99993 T=0.00007
ExAC Asian Sub 25154 C=0.99996 T=0.00004
ExAC American Sub 11578 C=0.99983 T=0.00017
ExAC African Sub 10400 C=0.99731 T=0.00269
ExAC Other Sub 908 C=1.000 T=0.000
The PAGE Study Global Study-wide 78702 C=0.99915 T=0.00085
The PAGE Study AfricanAmerican Sub 32516 C=0.99828 T=0.00172
The PAGE Study Mexican Sub 10810 C=1.00000 T=0.00000
The PAGE Study Asian Sub 8318 C=1.0000 T=0.0000
The PAGE Study PuertoRican Sub 7918 C=0.9997 T=0.0003
The PAGE Study NativeHawaiian Sub 4534 C=1.0000 T=0.0000
The PAGE Study Cuban Sub 4230 C=0.9998 T=0.0002
The PAGE Study Dominican Sub 3828 C=0.9997 T=0.0003
The PAGE Study CentralAmerican Sub 2450 C=0.9976 T=0.0024
The PAGE Study SouthAmerican Sub 1982 C=0.9995 T=0.0005
The PAGE Study NativeAmerican Sub 1260 C=1.0000 T=0.0000
The PAGE Study SouthAsian Sub 856 C=1.000 T=0.000
GO Exome Sequencing Project Global Study-wide 13006 C=0.99900 T=0.00100
GO Exome Sequencing Project European American Sub 8600 C=1.0000 T=0.0000
GO Exome Sequencing Project African American Sub 4406 C=0.9970 T=0.0030
1000Genomes_30x Global Study-wide 6404 C=0.9991 T=0.0009
1000Genomes_30x African Sub 1786 C=0.9966 T=0.0034
1000Genomes_30x Europe Sub 1266 C=1.0000 T=0.0000
1000Genomes_30x South Asian Sub 1202 C=1.0000 T=0.0000
1000Genomes_30x East Asian Sub 1170 C=1.0000 T=0.0000
1000Genomes_30x American Sub 980 C=1.000 T=0.000
1000Genomes Global Study-wide 5008 C=0.9994 T=0.0006
1000Genomes African Sub 1322 C=0.9977 T=0.0023
1000Genomes East Asian Sub 1008 C=1.0000 T=0.0000
1000Genomes Europe Sub 1006 C=1.0000 T=0.0000
1000Genomes South Asian Sub 978 C=1.000 T=0.000
1000Genomes American Sub 694 C=1.000 T=0.000
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=1.0000 T=0.0000
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.9997 T=0.0003
SGDP_PRJ Global Study-wide 2 C=0.5 T=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 7 NC_000007.14:g.94428379C>A
GRCh38.p14 chr 7 NC_000007.14:g.94428379C>T
GRCh37.p13 chr 7 NC_000007.13:g.94057691C>A
GRCh37.p13 chr 7 NC_000007.13:g.94057691C>T
COL1A2 RefSeqGene (LRG_2) NG_007405.1:g.38819C>A
COL1A2 RefSeqGene (LRG_2) NG_007405.1:g.38819C>T
Gene: COL1A2, collagen type I alpha 2 chain (plus strand)
Molecule type Change Amino acid[Codon] SO Term
COL1A2 transcript NM_000089.4:c.3613C>A R [CGG] > R [AGG] Coding Sequence Variant
collagen alpha-2(I) chain precursor NP_000080.2:p.Arg1205= R (Arg) > R (Arg) Synonymous Variant
COL1A2 transcript NM_000089.4:c.3613C>T R [CGG] > W [TGG] Coding Sequence Variant
collagen alpha-2(I) chain precursor NP_000080.2:p.Arg1205Trp R (Arg) > W (Trp) Missense 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: T (allele ID: 585544 )
ClinVar Accession Disease Names Clinical Significance
RCV000729778.6 not provided Conflicting-Interpretations-Of-Pathogenicity
RCV002233736.4 Ehlers-Danlos syndrome, classic type, 1,Osteogenesis imperfecta type I Likely-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 C= A T
GRCh38.p14 chr 7 NC_000007.14:g.94428379= NC_000007.14:g.94428379C>A NC_000007.14:g.94428379C>T
GRCh37.p13 chr 7 NC_000007.13:g.94057691= NC_000007.13:g.94057691C>A NC_000007.13:g.94057691C>T
COL1A2 RefSeqGene (LRG_2) NG_007405.1:g.38819= NG_007405.1:g.38819C>A NG_007405.1:g.38819C>T
COL1A2 transcript NM_000089.4:c.3613= NM_000089.4:c.3613C>A NM_000089.4:c.3613C>T
COL1A2 transcript NM_000089.3:c.3613= NM_000089.3:c.3613C>A NM_000089.3:c.3613C>T
collagen alpha-2(I) chain precursor NP_000080.2:p.Arg1205= NP_000080.2:p.Arg1205= NP_000080.2:p.Arg1205Trp
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#.

42 SubSNP, 13 Frequency, 2 ClinVar submissions
No Submitter Submission ID Date (Build)
1 NHLBI-ESP ss342239611 May 09, 2011 (134)
2 1000GENOMES ss488866908 May 04, 2012 (137)
3 EXOME_CHIP ss491401812 May 04, 2012 (137)
4 ILLUMINA ss780861365 Sep 08, 2015 (146)
5 ILLUMINA ss783545815 Sep 08, 2015 (146)
6 1000GENOMES ss1326197170 Aug 21, 2014 (142)
7 EVA_UK10K_ALSPAC ss1618726194 Apr 01, 2015 (144)
8 EVA_UK10K_TWINSUK ss1661720227 Apr 01, 2015 (144)
9 EVA_EXAC ss1688821675 Apr 01, 2015 (144)
10 ILLUMINA ss1752700729 Sep 08, 2015 (146)
11 ILLUMINA ss1917819094 Feb 12, 2016 (147)
12 ILLUMINA ss1946214388 Feb 12, 2016 (147)
13 ILLUMINA ss1959032741 Feb 12, 2016 (147)
14 HUMAN_LONGEVITY ss2295914552 Dec 20, 2016 (150)
15 GNOMAD ss2736568032 Nov 08, 2017 (151)
16 GNOMAD ss2747862339 Nov 08, 2017 (151)
17 GNOMAD ss2856351700 Nov 08, 2017 (151)
18 AFFY ss2985412717 Nov 08, 2017 (151)
19 ILLUMINA ss3022757720 Nov 08, 2017 (151)
20 ILLUMINA ss3629865732 Oct 12, 2018 (152)
21 ILLUMINA ss3635131184 Oct 12, 2018 (152)
22 ILLUMINA ss3640838476 Oct 12, 2018 (152)
23 ILLUMINA ss3644947483 Oct 12, 2018 (152)
24 ILLUMINA ss3653291602 Oct 12, 2018 (152)
25 ILLUMINA ss3654174249 Oct 12, 2018 (152)
26 ILLUMINA ss3726462625 Jul 13, 2019 (153)
27 ILLUMINA ss3744570046 Jul 13, 2019 (153)
28 ILLUMINA ss3745431209 Jul 13, 2019 (153)
29 PAGE_CC ss3771384168 Jul 13, 2019 (153)
30 ILLUMINA ss3772924093 Jul 13, 2019 (153)
31 EVA ss3824292249 Apr 26, 2020 (154)
32 SGDP_PRJ ss3867909124 Apr 26, 2020 (154)
33 TOPMED ss4755311487 Apr 26, 2021 (155)
34 TOPMED ss4755311488 Apr 26, 2021 (155)
35 1000G_HIGH_COVERAGE ss5273905350 Oct 13, 2022 (156)
36 EVA ss5375273720 Oct 13, 2022 (156)
37 HUGCELL_USP ss5470889654 Oct 13, 2022 (156)
38 1000G_HIGH_COVERAGE ss5562622872 Oct 13, 2022 (156)
39 SANFORD_IMAGENETICS ss5643517303 Oct 13, 2022 (156)
40 EVA ss5848145536 Oct 13, 2022 (156)
41 EVA ss5859945003 Oct 13, 2022 (156)
42 EVA ss5972698146 Oct 13, 2022 (156)
43 1000Genomes NC_000007.13 - 94057691 Oct 12, 2018 (152)
44 1000Genomes_30x NC_000007.14 - 94428379 Oct 13, 2022 (156)
45 The Avon Longitudinal Study of Parents and Children NC_000007.13 - 94057691 Oct 12, 2018 (152)
46 ExAC NC_000007.13 - 94057691 Oct 12, 2018 (152)
47 gnomAD - Genomes NC_000007.14 - 94428379 Apr 26, 2021 (155)
48 gnomAD - Exomes NC_000007.13 - 94057691 Jul 13, 2019 (153)
49 GO Exome Sequencing Project NC_000007.13 - 94057691 Oct 12, 2018 (152)
50 The PAGE Study NC_000007.14 - 94428379 Jul 13, 2019 (153)
51 SGDP_PRJ NC_000007.13 - 94057691 Apr 26, 2020 (154)
52 TopMed

Submission ignored due to conflicting rows:
Row 592689046 (NC_000007.14:94428378:C:A 1/264690)
Row 592689047 (NC_000007.14:94428378:C:T 169/264690)

- Apr 26, 2021 (155)
53 TopMed

Submission ignored due to conflicting rows:
Row 592689046 (NC_000007.14:94428378:C:A 1/264690)
Row 592689047 (NC_000007.14:94428378:C:T 169/264690)

- Apr 26, 2021 (155)
54 UK 10K study - Twins NC_000007.13 - 94057691 Oct 12, 2018 (152)
55 ALFA NC_000007.14 - 94428379 Apr 26, 2021 (155)
56 ClinVar RCV000729778.6 Oct 13, 2022 (156)
57 ClinVar RCV002233736.4 Oct 13, 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
ss2747862339, ss2856351700 NC_000007.13:94057690:C:A NC_000007.14:94428378:C:A (self)
12407073395, ss4755311487 NC_000007.14:94428378:C:A NC_000007.14:94428378:C:A (self)
38205811, 21260124, 8893960, 5731164, 750198, 19926104, 21260124, ss342239611, ss488866908, ss491401812, ss780861365, ss783545815, ss1326197170, ss1618726194, ss1661720227, ss1688821675, ss1752700729, ss1917819094, ss1946214388, ss1959032741, ss2736568032, ss2747862339, ss2856351700, ss2985412717, ss3022757720, ss3629865732, ss3635131184, ss3640838476, ss3644947483, ss3653291602, ss3654174249, ss3744570046, ss3745431209, ss3772924093, ss3824292249, ss3867909124, ss5375273720, ss5643517303, ss5848145536, ss5972698146 NC_000007.13:94057690:C:T NC_000007.14:94428378:C:T (self)
RCV000729778.6, RCV002233736.4, 50148807, 269581756, 605637, 12407073395, ss2295914552, ss3726462625, ss3771384168, ss4755311488, ss5273905350, ss5470889654, ss5562622872, ss5859945003 NC_000007.14:94428378:C:T NC_000007.14:94428378:C:T (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 rs150124840

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