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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs25388

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr15:48610768 (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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.003412 (903/264690, TOPMED)
A=0.003739 (940/251436, GnomAD_exome)
A=0.003722 (522/140240, GnomAD) (+ 17 more)
A=0.004086 (495/121146, ExAC)
A=0.00438 (217/49560, ALFA)
A=0.00493 (64/12986, GO-ESP)
A=0.0006 (4/6404, 1000G_30x)
A=0.0008 (4/5008, 1000G)
A=0.0027 (12/4480, Estonian)
A=0.0057 (22/3854, ALSPAC)
A=0.0073 (27/3708, TWINSUK)
A=0.007 (7/998, GoNL)
A=0.010 (6/600, NorthernSweden)
A=0.006 (3/534, MGP)
A=0.010 (3/304, FINRISK)
A=0.03 (1/40, GENOME_DK)
G=0.5 (1/2, SGDP_PRJ)
A=0.5 (1/2, SGDP_PRJ)
G=0.5 (1/2, Siberian)
A=0.5 (1/2, Siberian)
Clinical Significance
Reported in ClinVar
Gene : Consequence
FBN1 : Stop Gained
Publications
5 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: 20231103111315
Population Group Sample Size Ref Allele Alt Allele Ref HMOZ Alt HMOZ HTRZ HWEP
Total Global 65922 G=0.99546 A=0.00454 0.99105 0.000121 0.008829 9
European Sub 47336 G=0.99482 A=0.00518 0.989775 0.000127 0.010098 5
African Sub 8422 G=0.9989 A=0.0011 0.9981 0.000237 0.001662 32
African Others Sub 306 G=1.000 A=0.000 1.0 0.0 0.0 N/A
African American Sub 8116 G=0.9989 A=0.0011 0.998029 0.000246 0.001725 32
Asian Sub 172 G=1.000 A=0.000 1.0 0.0 0.0 N/A
East Asian Sub 114 G=1.000 A=0.000 1.0 0.0 0.0 N/A
Other Asian Sub 58 G=1.00 A=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 508 G=1.000 A=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 634 G=0.995 A=0.005 0.990536 0.0 0.009464 0
South Asian Sub 98 G=1.00 A=0.00 1.0 0.0 0.0 N/A
Other Sub 8752 G=0.9952 A=0.0048 0.990402 0.0 0.009598 0


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=0.996588 A=0.003412
gnomAD - Exomes Global Study-wide 251436 G=0.996261 A=0.003739
gnomAD - Exomes European Sub 135374 G=0.993869 A=0.006131
gnomAD - Exomes Asian Sub 49004 G=0.99980 A=0.00020
gnomAD - Exomes American Sub 34586 G=0.99864 A=0.00136
gnomAD - Exomes African Sub 16256 G=0.99926 A=0.00074
gnomAD - Exomes Ashkenazi Jewish Sub 10076 G=0.99861 A=0.00139
gnomAD - Exomes Other Sub 6140 G=0.9956 A=0.0044
gnomAD - Genomes Global Study-wide 140240 G=0.996278 A=0.003722
gnomAD - Genomes European Sub 75946 G=0.99413 A=0.00587
gnomAD - Genomes African Sub 42030 G=0.99895 A=0.00105
gnomAD - Genomes American Sub 13660 G=0.99854 A=0.00146
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=0.9994 A=0.0006
gnomAD - Genomes East Asian Sub 3128 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2152 G=0.9954 A=0.0046
ExAC Global Study-wide 121146 G=0.995914 A=0.004086
ExAC Europe Sub 73246 G=0.99368 A=0.00632
ExAC Asian Sub 25062 G=0.99976 A=0.00024
ExAC American Sub 11534 G=0.99879 A=0.00121
ExAC African Sub 10400 G=0.99894 A=0.00106
ExAC Other Sub 904 G=0.999 A=0.001
Allele Frequency Aggregator Total Global 49560 G=0.99562 A=0.00438
Allele Frequency Aggregator European Sub 37246 G=0.99514 A=0.00486
Allele Frequency Aggregator Other Sub 7318 G=0.9959 A=0.0041
Allele Frequency Aggregator African Sub 3584 G=0.9992 A=0.0008
Allele Frequency Aggregator Latin American 2 Sub 634 G=0.995 A=0.005
Allele Frequency Aggregator Latin American 1 Sub 508 G=1.000 A=0.000
Allele Frequency Aggregator Asian Sub 172 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 98 G=1.00 A=0.00
GO Exome Sequencing Project Global Study-wide 12986 G=0.99507 A=0.00493
GO Exome Sequencing Project European American Sub 8592 G=0.9930 A=0.0070
GO Exome Sequencing Project African American Sub 4394 G=0.9991 A=0.0009
1000Genomes_30x Global Study-wide 6404 G=0.9994 A=0.0006
1000Genomes_30x African Sub 1786 G=0.9994 A=0.0006
1000Genomes_30x Europe Sub 1266 G=0.9976 A=0.0024
1000Genomes_30x South Asian Sub 1202 G=1.0000 A=0.0000
1000Genomes_30x East Asian Sub 1170 G=1.0000 A=0.0000
1000Genomes_30x American Sub 980 G=1.000 A=0.000
1000Genomes Global Study-wide 5008 G=0.9992 A=0.0008
1000Genomes African Sub 1322 G=0.9992 A=0.0008
1000Genomes East Asian Sub 1008 G=1.0000 A=0.0000
1000Genomes Europe Sub 1006 G=0.9970 A=0.0030
1000Genomes South Asian Sub 978 G=1.000 A=0.000
1000Genomes American Sub 694 G=1.000 A=0.000
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.9973 A=0.0027
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.9943 A=0.0057
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.9927 A=0.0073
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.993 A=0.007
Northern Sweden ACPOP Study-wide 600 G=0.990 A=0.010
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 G=0.994 A=0.006
FINRISK Finnish from FINRISK project Study-wide 304 G=0.990 A=0.010
The Danish reference pan genome Danish Study-wide 40 G=0.97 A=0.03
SGDP_PRJ Global Study-wide 2 G=0.5 A=0.5
Siberian Global Study-wide 2 G=0.5 A=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 15 NC_000015.10:g.48610768G>A
GRCh38.p14 chr 15 NC_000015.10:g.48610768G>T
GRCh37.p13 chr 15 NC_000015.9:g.48902965G>A
GRCh37.p13 chr 15 NC_000015.9:g.48902965G>T
FBN1 RefSeqGene (LRG_778) NG_008805.2:g.40021C>T
FBN1 RefSeqGene (LRG_778) NG_008805.2:g.40021C>A
Gene: FBN1, fibrillin 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
FBN1 transcript variant 1 NM_000138.5:c.306C>T C [TGC] > C [TGT] Coding Sequence Variant
fibrillin-1 isoform a preproprotein NP_000129.3:p.Cys102= C (Cys) > C (Cys) Synonymous Variant
FBN1 transcript variant 1 NM_000138.5:c.306C>A C [TGC] > * [TGA] Coding Sequence Variant
fibrillin-1 isoform a preproprotein NP_000129.3:p.Cys102Ter C (Cys) > * (Ter) Stop Gained
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: A (allele ID: 141017 )
ClinVar Accession Disease Names Clinical Significance
RCV000154417.12 not specified Benign
RCV000253616.8 Familial thoracic aortic aneurysm and aortic dissection Benign-Likely-Benign
RCV000293746.4 Ectopia lentis 1, isolated, autosomal dominant Benign
RCV000313423.4 Weill-Marchesani syndrome Benign
RCV000347453.4 Stiff skin syndrome Benign
RCV000348609.4 Marfan syndrome Benign
RCV000382318.4 Geleophysic dysplasia Benign
RCV000407439.4 Acromicric dysplasia Benign
RCV000617060.2 Cardiovascular phenotype Likely-Benign
RCV000659501.3 Connective tissue disorder Likely-Benign
RCV000756133.9 Familial thoracic aortic aneurysm and aortic dissection,Marfan syndrome Benign
RCV001725986.6 not provided Benign
Allele: T (allele ID: 374628 )
ClinVar Accession Disease Names Clinical Significance
RCV000441111.1 not provided Likely-Pathogenic
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 T
GRCh38.p14 chr 15 NC_000015.10:g.48610768= NC_000015.10:g.48610768G>A NC_000015.10:g.48610768G>T
GRCh37.p13 chr 15 NC_000015.9:g.48902965= NC_000015.9:g.48902965G>A NC_000015.9:g.48902965G>T
FBN1 RefSeqGene (LRG_778) NG_008805.2:g.40021= NG_008805.2:g.40021C>T NG_008805.2:g.40021C>A
FBN1 transcript variant 1 NM_000138.5:c.306= NM_000138.5:c.306C>T NM_000138.5:c.306C>A
FBN1 transcript NM_000138.4:c.306= NM_000138.4:c.306C>T NM_000138.4:c.306C>A
FBN1 transcript variant 2 NM_001406716.1:c.306= NM_001406716.1:c.306C>T NM_001406716.1:c.306C>A
FBN1 transcript variant 3 NM_001406717.1:c.306= NM_001406717.1:c.306C>T NM_001406717.1:c.306C>A
fibrillin-1 isoform a preproprotein NP_000129.3:p.Cys102= NP_000129.3:p.Cys102= NP_000129.3:p.Cys102Ter
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#.

43 SubSNP, 18 Frequency, 13 ClinVar submissions
No Submitter Submission ID Date (Build)
1 OEFNER ss28104 Jan 19, 2000 (69)
2 RSG_UW ss212965218 Jul 04, 2010 (132)
3 1000GENOMES ss338763499 May 09, 2011 (134)
4 NHLBI-ESP ss342403269 May 09, 2011 (134)
5 1000GENOMES ss491082842 May 04, 2012 (137)
6 CLINSEQ_SNP ss491700444 May 04, 2012 (137)
7 ILLUMINA ss534856821 Sep 08, 2015 (146)
8 EVA-GONL ss991762297 Aug 21, 2014 (142)
9 1000GENOMES ss1353370922 Aug 21, 2014 (142)
10 CLINVAR ss1457617520 Nov 23, 2014 (142)
11 EVA_GENOME_DK ss1577599570 Apr 01, 2015 (144)
12 EVA_FINRISK ss1584093903 Apr 01, 2015 (144)
13 EVA_UK10K_ALSPAC ss1632946941 Apr 01, 2015 (144)
14 EVA_UK10K_TWINSUK ss1675940974 Apr 01, 2015 (144)
15 EVA_EXAC ss1691820730 Apr 01, 2015 (144)
16 EVA_DECODE ss1695778555 Apr 01, 2015 (144)
17 EVA_MGP ss1711396967 Apr 01, 2015 (144)
18 JJLAB ss2028362132 Sep 14, 2016 (149)
19 CLINVAR ss2137502291 Apr 13, 2017 (150)
20 CLINVAR ss2137508645 Apr 18, 2017 (150)
21 USC_VALOUEV ss2156763263 Dec 20, 2016 (150)
22 HUMAN_LONGEVITY ss2206582761 Dec 20, 2016 (150)
23 GNOMAD ss2741233308 Nov 08, 2017 (151)
24 GNOMAD ss2749301473 Nov 08, 2017 (151)
25 GNOMAD ss2934636671 Nov 08, 2017 (151)
26 SWEGEN ss3013244421 Nov 08, 2017 (151)
27 ILLUMINA ss3627355591 Oct 12, 2018 (152)
28 EGCUT_WGS ss3680385385 Jul 13, 2019 (153)
29 EVA_DECODE ss3697846489 Jul 13, 2019 (153)
30 ACPOP ss3740902745 Jul 13, 2019 (153)
31 EVA ss3824917939 Apr 27, 2020 (154)
32 EVA ss3825858742 Apr 27, 2020 (154)
33 SGDP_PRJ ss3882868292 Apr 27, 2020 (154)
34 EVA ss3986647749 Apr 27, 2021 (155)
35 TOPMED ss4990559079 Apr 27, 2021 (155)
36 1000G_HIGH_COVERAGE ss5298360671 Oct 16, 2022 (156)
37 EVA ss5419090509 Oct 16, 2022 (156)
38 HUGCELL_USP ss5492098267 Oct 16, 2022 (156)
39 1000G_HIGH_COVERAGE ss5599724079 Oct 16, 2022 (156)
40 EVA ss5828170391 Oct 16, 2022 (156)
41 EVA ss5848401711 Oct 16, 2022 (156)
42 EVA ss5875782900 Oct 16, 2022 (156)
43 EVA ss5948862283 Oct 16, 2022 (156)
44 1000Genomes NC_000015.9 - 48902965 Oct 12, 2018 (152)
45 1000Genomes_30x NC_000015.10 - 48610768 Oct 16, 2022 (156)
46 The Avon Longitudinal Study of Parents and Children NC_000015.9 - 48902965 Oct 12, 2018 (152)
47 Genetic variation in the Estonian population NC_000015.9 - 48902965 Oct 12, 2018 (152)
48 ExAC NC_000015.9 - 48902965 Oct 12, 2018 (152)
49 FINRISK NC_000015.9 - 48902965 Apr 27, 2020 (154)
50 The Danish reference pan genome NC_000015.9 - 48902965 Apr 27, 2020 (154)
51 gnomAD - Genomes NC_000015.10 - 48610768 Apr 27, 2021 (155)
52 gnomAD - Exomes NC_000015.9 - 48902965 Jul 13, 2019 (153)
53 GO Exome Sequencing Project NC_000015.9 - 48902965 Oct 12, 2018 (152)
54 Genome of the Netherlands Release 5 NC_000015.9 - 48902965 Apr 27, 2020 (154)
55 Medical Genome Project healthy controls from Spanish population NC_000015.9 - 48902965 Apr 27, 2020 (154)
56 Northern Sweden NC_000015.9 - 48902965 Jul 13, 2019 (153)
57 SGDP_PRJ NC_000015.9 - 48902965 Apr 27, 2020 (154)
58 Siberian NC_000015.9 - 48902965 Apr 27, 2020 (154)
59 TopMed NC_000015.10 - 48610768 Apr 27, 2021 (155)
60 UK 10K study - Twins NC_000015.9 - 48902965 Oct 12, 2018 (152)
61 ALFA NC_000015.10 - 48610768 Apr 27, 2021 (155)
62 ClinVar RCV000154417.12 Oct 16, 2022 (156)
63 ClinVar RCV000253616.8 Oct 16, 2022 (156)
64 ClinVar RCV000293746.4 Oct 16, 2022 (156)
65 ClinVar RCV000313423.4 Oct 16, 2022 (156)
66 ClinVar RCV000347453.4 Oct 16, 2022 (156)
67 ClinVar RCV000348609.4 Oct 16, 2022 (156)
68 ClinVar RCV000382318.4 Oct 16, 2022 (156)
69 ClinVar RCV000407439.4 Oct 16, 2022 (156)
70 ClinVar RCV000441111.1 Oct 12, 2018 (152)
71 ClinVar RCV000617060.2 Oct 16, 2022 (156)
72 ClinVar RCV000659501.3 Oct 16, 2022 (156)
73 ClinVar RCV000756133.9 Oct 16, 2022 (156)
74 ClinVar RCV001725986.6 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
ss491700444, ss1695778555 NC_000015.8:46690256:G:A NC_000015.10:48610767:G:A (self)
66439417, 36880348, 26123633, 2193709, 90364, 3846021, 10498603, 1375212, 16471393, 512727, 14187610, 34885272, 9279617, 36880348, ss338763499, ss342403269, ss491082842, ss534856821, ss991762297, ss1353370922, ss1577599570, ss1584093903, ss1632946941, ss1675940974, ss1691820730, ss1711396967, ss2028362132, ss2156763263, ss2741233308, ss2749301473, ss2934636671, ss3013244421, ss3627355591, ss3680385385, ss3740902745, ss3824917939, ss3825858742, ss3882868292, ss3986647749, ss5419090509, ss5828170391, ss5848401711, ss5948862283 NC_000015.9:48902964:G:A NC_000015.10:48610767:G:A (self)
RCV000154417.12, RCV000253616.8, RCV000293746.4, RCV000313423.4, RCV000347453.4, RCV000348609.4, RCV000382318.4, RCV000407439.4, RCV000617060.2, RCV000659501.3, RCV000756133.9, RCV001725986.6, 87250014, 468384951, 206104739, 2012326930, ss1457617520, ss2206582761, ss3697846489, ss4990559079, ss5298360671, ss5492098267, ss5599724079, ss5875782900 NC_000015.10:48610767:G:A NC_000015.10:48610767:G:A (self)
ss28104, ss212965218 NT_010194.17:19693521:G:A NC_000015.10:48610767:G:A (self)
RCV000441111.1, ss2137502291, ss2137508645 NC_000015.10:48610767:G:T NC_000015.10:48610767:G:T (self)
Help

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

5 citations for rs25388
PMID Title Author Year Journal
11933199 Evaluation and application of denaturing HPLC for mutation detection in Marfan syndrome: Identification of 20 novel mutations and two novel polymorphisms in the FBN1 gene. Mátyás G et al. 2002 Human mutation
12161601 Twelve novel FBN1 mutations in Marfan syndrome and Marfan related phenotypes test the feasibility of FBN1 mutation testing in clinical practice. Halliday DJ et al. 2002 Journal of medical genetics
16220557 Identification of 29 novel and nine recurrent fibrillin-1 (FBN1) mutations and genotype-phenotype correlations in 76 patients with Marfan syndrome. Rommel K et al. 2005 Human mutation
24033266 A systematic approach to assessing the clinical significance of genetic variants. Duzkale H et al. 2013 Clinical genetics
25741868 Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Richards S et al. 2015 Genetics in medicine
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.post825+45319f0