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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.

rs73390532

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr18:6959403 (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
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.008746 (2315/264690, TOPMED)
A=0.001945 (489/251450, GnomAD_exome)
A=0.008108 (1137/140226, GnomAD) (+ 10 more)
A=0.002512 (305/121408, ExAC)
A=0.00207 (116/56142, ALFA)
A=0.00815 (106/13006, GO-ESP)
A=0.0092 (59/6404, 1000G_30x)
A=0.0092 (46/5008, 1000G)
A=0.0002 (1/4480, Estonian)
A=0.002 (1/534, MGP)
A=0.009 (2/216, Qatari)
G=0.5 (3/6, SGDP_PRJ)
A=0.5 (3/6, SGDP_PRJ)
Clinical Significance
Reported in ClinVar
Gene : Consequence
LAMA1 : Synonymous 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 72502 G=0.99670 A=0.00330
European Sub 53350 G=0.99983 A=0.00017
African Sub 8632 G=0.9756 A=0.0244
African Others Sub 316 G=0.959 A=0.041
African American Sub 8316 G=0.9762 A=0.0238
Asian Sub 184 G=1.000 A=0.000
East Asian Sub 126 G=1.000 A=0.000
Other Asian Sub 58 G=1.00 A=0.00
Latin American 1 Sub 522 G=0.994 A=0.006
Latin American 2 Sub 718 G=0.997 A=0.003
South Asian Sub 114 G=1.000 A=0.000
Other Sub 8982 G=0.9984 A=0.0016


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=0.991254 A=0.008746
gnomAD - Exomes Global Study-wide 251450 G=0.998055 A=0.001945
gnomAD - Exomes European Sub 135378 G=0.999919 A=0.000081
gnomAD - Exomes Asian Sub 49010 G=0.99994 A=0.00006
gnomAD - Exomes American Sub 34592 G=0.99850 A=0.00150
gnomAD - Exomes African Sub 16254 G=0.97453 A=0.02547
gnomAD - Exomes Ashkenazi Jewish Sub 10078 G=0.99990 A=0.00010
gnomAD - Exomes Other Sub 6138 G=0.9987 A=0.0013
gnomAD - Genomes Global Study-wide 140226 G=0.991892 A=0.008108
gnomAD - Genomes European Sub 75954 G=0.99989 A=0.00011
gnomAD - Genomes African Sub 42004 G=0.97507 A=0.02493
gnomAD - Genomes American Sub 13658 G=0.99509 A=0.00491
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3134 G=0.9997 A=0.0003
gnomAD - Genomes Other Sub 2152 G=0.9935 A=0.0065
ExAC Global Study-wide 121408 G=0.997488 A=0.002512
ExAC Europe Sub 73350 G=0.99993 A=0.00007
ExAC Asian Sub 25166 G=0.99992 A=0.00008
ExAC American Sub 11578 G=0.99870 A=0.00130
ExAC African Sub 10406 G=0.97290 A=0.02710
ExAC Other Sub 908 G=0.999 A=0.001
Allele Frequency Aggregator Total Global 56142 G=0.99793 A=0.00207
Allele Frequency Aggregator European Sub 43260 G=0.99979 A=0.00021
Allele Frequency Aggregator Other Sub 7548 G=0.9987 A=0.0013
Allele Frequency Aggregator African Sub 3796 G=0.9758 A=0.0242
Allele Frequency Aggregator Latin American 2 Sub 718 G=0.997 A=0.003
Allele Frequency Aggregator Latin American 1 Sub 522 G=0.994 A=0.006
Allele Frequency Aggregator Asian Sub 184 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 114 G=1.000 A=0.000
GO Exome Sequencing Project Global Study-wide 13006 G=0.99185 A=0.00815
GO Exome Sequencing Project European American Sub 8600 G=0.9997 A=0.0003
GO Exome Sequencing Project African American Sub 4406 G=0.9766 A=0.0234
1000Genomes_30x Global Study-wide 6404 G=0.9908 A=0.0092
1000Genomes_30x African Sub 1786 G=0.9709 A=0.0291
1000Genomes_30x Europe Sub 1266 G=1.0000 A=0.0000
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=0.993 A=0.007
1000Genomes Global Study-wide 5008 G=0.9908 A=0.0092
1000Genomes African Sub 1322 G=0.9705 A=0.0295
1000Genomes East Asian Sub 1008 G=0.9990 A=0.0010
1000Genomes Europe Sub 1006 G=0.9990 A=0.0010
1000Genomes South Asian Sub 978 G=1.000 A=0.000
1000Genomes American Sub 694 G=0.993 A=0.007
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.9998 A=0.0002
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 G=0.998 A=0.002
Qatari Global Study-wide 216 G=0.991 A=0.009
SGDP_PRJ Global Study-wide 6 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 18 NC_000018.10:g.6959403G>A
GRCh37.p13 chr 18 NC_000018.9:g.6959402G>A
LAMA1 RefSeqGene NG_034251.1:g.163412C>T
Gene: LAMA1, laminin subunit alpha 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LAMA1 transcript NM_005559.4:c.7716C>T H [CAC] > H [CAT] Coding Sequence Variant
laminin subunit alpha-1 precursor NP_005550.2:p.His2572= H (His) > H (His) Synonymous 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: A (allele ID: 716037 )
ClinVar Accession Disease Names Clinical Significance
RCV000968365.6 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
GRCh38.p14 chr 18 NC_000018.10:g.6959403= NC_000018.10:g.6959403G>A
GRCh37.p13 chr 18 NC_000018.9:g.6959402= NC_000018.9:g.6959402G>A
LAMA1 RefSeqGene NG_034251.1:g.163412= NG_034251.1:g.163412C>T
LAMA1 transcript NM_005559.4:c.7716= NM_005559.4:c.7716C>T
LAMA1 transcript NM_005559.3:c.7716= NM_005559.3:c.7716C>T
laminin subunit alpha-1 precursor NP_005550.2:p.His2572= NP_005550.2:p.His2572=
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#.

44 SubSNP, 12 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss114021250 Feb 14, 2009 (130)
2 SEATTLESEQ ss159736887 Dec 01, 2009 (131)
3 COMPLETE_GENOMICS ss169015507 Jul 04, 2010 (132)
4 1000GENOMES ss227724897 Jul 14, 2010 (132)
5 NHLBI-ESP ss342470614 May 09, 2011 (134)
6 ILLUMINA ss481008446 May 04, 2012 (137)
7 ILLUMINA ss483772767 May 04, 2012 (137)
8 1000GENOMES ss491136413 May 04, 2012 (137)
9 ILLUMINA ss534077550 Sep 08, 2015 (146)
10 TISHKOFF ss565488162 Apr 25, 2013 (138)
11 ILLUMINA ss780644415 Sep 08, 2015 (146)
12 ILLUMINA ss781373716 Sep 08, 2015 (146)
13 ILLUMINA ss783599580 Sep 08, 2015 (146)
14 ILLUMINA ss836138944 Sep 08, 2015 (146)
15 JMKIDD_LAB ss1067577634 Aug 21, 2014 (142)
16 JMKIDD_LAB ss1081307596 Aug 21, 2014 (142)
17 1000GENOMES ss1360019007 Aug 21, 2014 (142)
18 EVA_EXAC ss1693073758 Apr 01, 2015 (144)
19 EVA_MGP ss1711479616 Apr 01, 2015 (144)
20 HAMMER_LAB ss1808941827 Sep 08, 2015 (146)
21 WEILL_CORNELL_DGM ss1936933153 Feb 12, 2016 (147)
22 HUMAN_LONGEVITY ss2219600366 Dec 20, 2016 (150)
23 ILLUMINA ss2633443301 Nov 08, 2017 (151)
24 GNOMAD ss2743176470 Nov 08, 2017 (151)
25 GNOMAD ss2749920323 Nov 08, 2017 (151)
26 GNOMAD ss2953801696 Nov 08, 2017 (151)
27 AFFY ss2985111230 Nov 08, 2017 (151)
28 ILLUMINA ss3627754138 Oct 12, 2018 (152)
29 ILLUMINA ss3631421310 Oct 12, 2018 (152)
30 EGCUT_WGS ss3682967678 Jul 13, 2019 (153)
31 KHV_HUMAN_GENOMES ss3820349659 Jul 13, 2019 (153)
32 EVA ss3825176863 Apr 27, 2020 (154)
33 EVA ss3825912519 Apr 27, 2020 (154)
34 SGDP_PRJ ss3886488222 Apr 27, 2020 (154)
35 FSA-LAB ss3984129175 Apr 27, 2021 (155)
36 TOPMED ss5047782972 Apr 27, 2021 (155)
37 1000G_HIGH_COVERAGE ss5304371743 Oct 16, 2022 (156)
38 TRAN_CS_UWATERLOO ss5314450059 Oct 16, 2022 (156)
39 EVA ss5429804701 Oct 16, 2022 (156)
40 HUGCELL_USP ss5497287504 Oct 16, 2022 (156)
41 1000G_HIGH_COVERAGE ss5608660985 Oct 16, 2022 (156)
42 SANFORD_IMAGENETICS ss5660790367 Oct 16, 2022 (156)
43 EVA ss5873086719 Oct 16, 2022 (156)
44 EVA ss5952190597 Oct 16, 2022 (156)
45 1000Genomes NC_000018.9 - 6959402 Oct 12, 2018 (152)
46 1000Genomes_30x NC_000018.10 - 6959403 Oct 16, 2022 (156)
47 Genetic variation in the Estonian population NC_000018.9 - 6959402 Oct 12, 2018 (152)
48 ExAC NC_000018.9 - 6959402 Oct 12, 2018 (152)
49 gnomAD - Genomes NC_000018.10 - 6959403 Apr 27, 2021 (155)
50 gnomAD - Exomes NC_000018.9 - 6959402 Jul 13, 2019 (153)
51 GO Exome Sequencing Project NC_000018.9 - 6959402 Oct 12, 2018 (152)
52 Medical Genome Project healthy controls from Spanish population NC_000018.9 - 6959402 Apr 27, 2020 (154)
53 Qatari NC_000018.9 - 6959402 Apr 27, 2020 (154)
54 SGDP_PRJ NC_000018.9 - 6959402 Apr 27, 2020 (154)
55 TopMed NC_000018.10 - 6959403 Apr 27, 2021 (155)
56 ALFA NC_000018.10 - 6959403 Apr 27, 2021 (155)
57 ClinVar RCV000968365.6 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
ss114021250, ss169015507, ss483772767 NC_000018.8:6949401:G:A NC_000018.10:6959402:G:A (self)
73312742, 28705926, 3539264, 12486023, 1633897, 595376, 18975075, 38505202, ss227724897, ss342470614, ss481008446, ss491136413, ss534077550, ss565488162, ss780644415, ss781373716, ss783599580, ss836138944, ss1067577634, ss1081307596, ss1360019007, ss1693073758, ss1711479616, ss1808941827, ss1936933153, ss2633443301, ss2743176470, ss2749920323, ss2953801696, ss2985111230, ss3627754138, ss3631421310, ss3682967678, ss3825176863, ss3825912519, ss3886488222, ss3984129175, ss5429804701, ss5660790367, ss5952190597 NC_000018.9:6959401:G:A NC_000018.10:6959402:G:A (self)
RCV000968365.6, 96186920, 517238884, 263328635, 4712375538, ss2219600366, ss3820349659, ss5047782972, ss5304371743, ss5314450059, ss5497287504, ss5608660985, ss5873086719 NC_000018.10:6959402:G:A NC_000018.10:6959402:G:A (self)
ss159736887 NT_010859.14:6949401:G:A NC_000018.10:6959402:G:A (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 rs73390532

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