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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.

rs390802

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr3:52397655 (GRCh38.p13) 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=0.163875 (43376/264690, TOPMED)
A=0.161744 (22660/140098, GnomAD)
A=0.16597 (4041/24348, ALFA) (+ 18 more)
A=0.02464 (413/16760, 8.3KJPN)
A=0.1328 (665/5008, 1000G)
A=0.1232 (552/4480, Estonian)
A=0.1793 (691/3854, ALSPAC)
A=0.1847 (685/3708, TWINSUK)
A=0.0382 (112/2930, KOREAN)
A=0.1475 (279/1892, HapMap)
A=0.0382 (70/1832, Korea1K)
A=0.172 (172/998, GoNL)
A=0.155 (93/600, NorthernSweden)
A=0.180 (96/534, MGP)
A=0.148 (32/216, Qatari)
A=0.052 (11/212, Vietnamese)
G=0.452 (66/146, SGDP_PRJ)
A=0.29 (20/68, Ancient Sardinia)
A=0.20 (8/40, GENOME_DK)
G=0.50 (6/12, Siberian)
A=0.50 (6/12, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
DNAH1 : Intron Variant
Publications
2 citations
Genomic View
See rs on genome
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.p13 chr 3 NC_000003.12:g.52397655G>A
GRCh37.p13 chr 3 NC_000003.11:g.52431671G>A
DNAH1 RefSeqGene NG_052911.1:g.86337G>A
Gene: DNAH1, dynein axonemal heavy chain 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
DNAH1 transcript NM_015512.5:c.11788-52G>A N/A Intron Variant
DNAH1 transcript variant X1 XM_017006129.1:c.11857-52…

XM_017006129.1:c.11857-52G>A

N/A Intron Variant
DNAH1 transcript variant X2 XM_017006130.1:c.11788-52…

XM_017006130.1:c.11788-52G>A

N/A Intron Variant
DNAH1 transcript variant X3 XM_017006131.1:c.11731-52…

XM_017006131.1:c.11731-52G>A

N/A Intron Variant
DNAH1 transcript variant X6 XM_017006132.1:c. N/A Genic Downstream Transcript Variant
DNAH1 transcript variant X7 XM_017006133.1:c. N/A Genic Downstream Transcript Variant
DNAH1 transcript variant X4 XR_001740098.1:n. N/A Intron Variant
DNAH1 transcript variant X5 XR_001740099.1:n. 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.

Not Reported in ClinVar

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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 24348 G=0.83403 A=0.16597
European Sub 18124 G=0.83563 A=0.16437
African Sub 4114 G=0.8121 A=0.1879
African Others Sub 148 G=0.838 A=0.162
African American Sub 3966 G=0.8111 A=0.1889
Asian Sub 124 G=0.976 A=0.024
East Asian Sub 96 G=1.00 A=0.00
Other Asian Sub 28 G=0.89 A=0.11
Latin American 1 Sub 168 G=0.810 A=0.190
Latin American 2 Sub 670 G=0.869 A=0.131
South Asian Sub 98 G=0.91 A=0.09
Other Sub 1050 G=0.8505 A=0.1495


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=0.836125 A=0.163875
gnomAD - Genomes Global Study-wide 140098 G=0.838256 A=0.161744
gnomAD - Genomes European Sub 75882 G=0.83805 A=0.16195
gnomAD - Genomes African Sub 41954 G=0.82185 A=0.17815
gnomAD - Genomes American Sub 13658 G=0.85979 A=0.14021
gnomAD - Genomes Ashkenazi Jewish Sub 3322 G=0.8414 A=0.1586
gnomAD - Genomes East Asian Sub 3130 G=0.9732 A=0.0268
gnomAD - Genomes Other Sub 2152 G=0.8276 A=0.1724
8.3KJPN JAPANESE Study-wide 16760 G=0.97536 A=0.02464
1000Genomes Global Study-wide 5008 G=0.8672 A=0.1328
1000Genomes African Sub 1322 G=0.7935 A=0.2065
1000Genomes East Asian Sub 1008 G=0.9732 A=0.0268
1000Genomes Europe Sub 1006 G=0.8360 A=0.1640
1000Genomes South Asian Sub 978 G=0.898 A=0.102
1000Genomes American Sub 694 G=0.856 A=0.144
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.8768 A=0.1232
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.8207 A=0.1793
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.8153 A=0.1847
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.9618 A=0.0382
HapMap Global Study-wide 1892 G=0.8525 A=0.1475
HapMap American Sub 770 G=0.875 A=0.125
HapMap African Sub 692 G=0.805 A=0.195
HapMap Asian Sub 254 G=0.969 A=0.031
HapMap Europe Sub 176 G=0.773 A=0.227
Korean Genome Project KOREAN Study-wide 1832 G=0.9618 A=0.0382
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.828 A=0.172
Northern Sweden ACPOP Study-wide 600 G=0.845 A=0.155
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 G=0.820 A=0.180
Qatari Global Study-wide 216 G=0.852 A=0.148
A Vietnamese Genetic Variation Database Global Study-wide 212 G=0.948 A=0.052
SGDP_PRJ Global Study-wide 146 G=0.452 A=0.548
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 68 G=0.71 A=0.29
The Danish reference pan genome Danish Study-wide 40 G=0.80 A=0.20
Siberian Global Study-wide 12 G=0.50 A=0.50
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.p13 chr 3 NC_000003.12:g.52397655= NC_000003.12:g.52397655G>A
GRCh37.p13 chr 3 NC_000003.11:g.52431671= NC_000003.11:g.52431671G>A
DNAH1 RefSeqGene NG_052911.1:g.86337= NG_052911.1:g.86337G>A
DNAH1 transcript NM_015512.4:c.11788-52= NM_015512.4:c.11788-52G>A
DNAH1 transcript NM_015512.5:c.11788-52= NM_015512.5:c.11788-52G>A
DNAH1 transcript variant X1 XM_017006129.1:c.11857-52= XM_017006129.1:c.11857-52G>A
DNAH1 transcript variant X2 XM_017006130.1:c.11788-52= XM_017006130.1:c.11788-52G>A
DNAH1 transcript variant X3 XM_017006131.1:c.11731-52= XM_017006131.1:c.11731-52G>A
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, 20 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss505389 Jul 16, 2000 (80)
2 KWOK ss993901 Oct 04, 2000 (86)
3 KWOK ss1059956 Oct 04, 2000 (86)
4 KWOK ss1838025 Oct 18, 2000 (87)
5 KWOK ss1856256 Oct 18, 2000 (87)
6 ABI ss44396218 Mar 14, 2006 (126)
7 ILLUMINA ss75146187 Dec 06, 2007 (129)
8 1000GENOMES ss111685553 Jan 25, 2009 (130)
9 ILLUMINA-UK ss117080693 Feb 14, 2009 (130)
10 KRIBB_YJKIM ss119352470 Dec 01, 2009 (131)
11 ILLUMINA ss173670328 Jul 04, 2010 (132)
12 BUSHMAN ss202509454 Jul 04, 2010 (132)
13 1000GENOMES ss220132040 Jul 14, 2010 (132)
14 1000GENOMES ss231817026 Jul 14, 2010 (132)
15 GMI ss277121969 May 04, 2012 (137)
16 ILLUMINA ss410847287 Sep 17, 2011 (135)
17 ILLUMINA ss537207552 Sep 08, 2015 (146)
18 TISHKOFF ss556608203 Apr 25, 2013 (138)
19 SSMP ss650286330 Apr 25, 2013 (138)
20 EVA-GONL ss978581167 Aug 21, 2014 (142)
21 JMKIDD_LAB ss1070400372 Aug 21, 2014 (142)
22 1000GENOMES ss1303968925 Aug 21, 2014 (142)
23 DDI ss1429416713 Apr 01, 2015 (144)
24 EVA_GENOME_DK ss1579958718 Apr 01, 2015 (144)
25 EVA_DECODE ss1588052214 Apr 01, 2015 (144)
26 EVA_UK10K_ALSPAC ss1607049897 Apr 01, 2015 (144)
27 EVA_UK10K_TWINSUK ss1650043930 Apr 01, 2015 (144)
28 EVA_MGP ss1711018843 Apr 01, 2015 (144)
29 EVA_SVP ss1712574790 Apr 01, 2015 (144)
30 WEILL_CORNELL_DGM ss1921821406 Feb 12, 2016 (147)
31 GENOMED ss1969389597 Jul 19, 2016 (147)
32 JJLAB ss2021469891 Sep 14, 2016 (149)
33 USC_VALOUEV ss2149543306 Dec 20, 2016 (150)
34 HUMAN_LONGEVITY ss2251507653 Dec 20, 2016 (150)
35 TOPMED ss2418582810 Dec 20, 2016 (150)
36 GRF ss2704916329 Nov 08, 2017 (151)
37 GNOMAD ss2792877201 Nov 08, 2017 (151)
38 SWEGEN ss2992301286 Nov 08, 2017 (151)
39 BIOINF_KMB_FNS_UNIBA ss3024496355 Nov 08, 2017 (151)
40 CSHL ss3345013705 Nov 08, 2017 (151)
41 TOPMED ss3390374559 Nov 08, 2017 (151)
42 ILLUMINA ss3628658591 Oct 12, 2018 (152)
43 ILLUMINA ss3638414395 Oct 12, 2018 (152)
44 ILLUMINA ss3643371490 Oct 12, 2018 (152)
45 OMUKHERJEE_ADBS ss3646286644 Oct 12, 2018 (152)
46 EGCUT_WGS ss3660222718 Jul 13, 2019 (153)
47 EVA_DECODE ss3709214425 Jul 13, 2019 (153)
48 ACPOP ss3729878331 Jul 13, 2019 (153)
49 EVA ss3760021541 Jul 13, 2019 (153)
50 KHV_HUMAN_GENOMES ss3803158738 Jul 13, 2019 (153)
51 EVA ss3825634334 Apr 25, 2020 (154)
52 EVA ss3827803869 Apr 25, 2020 (154)
53 SGDP_PRJ ss3855827560 Apr 25, 2020 (154)
54 KRGDB ss3901682455 Apr 25, 2020 (154)
55 KOGIC ss3951252200 Apr 25, 2020 (154)
56 FSA-LAB ss3984251432 Apr 26, 2021 (155)
57 FSA-LAB ss3984251433 Apr 26, 2021 (155)
58 EVA ss3984990208 Apr 26, 2021 (155)
59 EVA ss3986240670 Apr 26, 2021 (155)
60 EVA ss4017080397 Apr 26, 2021 (155)
61 TOPMED ss4564428985 Apr 26, 2021 (155)
62 TOMMO_GENOMICS ss5159127365 Apr 26, 2021 (155)
63 1000Genomes NC_000003.11 - 52431671 Oct 12, 2018 (152)
64 The Avon Longitudinal Study of Parents and Children NC_000003.11 - 52431671 Oct 12, 2018 (152)
65 Genetic variation in the Estonian population NC_000003.11 - 52431671 Oct 12, 2018 (152)
66 The Danish reference pan genome NC_000003.11 - 52431671 Apr 25, 2020 (154)
67 gnomAD - Genomes NC_000003.12 - 52397655 Apr 26, 2021 (155)
68 Genome of the Netherlands Release 5 NC_000003.11 - 52431671 Apr 25, 2020 (154)
69 HapMap NC_000003.12 - 52397655 Apr 25, 2020 (154)
70 KOREAN population from KRGDB NC_000003.11 - 52431671 Apr 25, 2020 (154)
71 Korean Genome Project NC_000003.12 - 52397655 Apr 25, 2020 (154)
72 Medical Genome Project healthy controls from Spanish population NC_000003.11 - 52431671 Apr 25, 2020 (154)
73 Northern Sweden NC_000003.11 - 52431671 Jul 13, 2019 (153)
74 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000003.11 - 52431671 Apr 26, 2021 (155)
75 Qatari NC_000003.11 - 52431671 Apr 25, 2020 (154)
76 SGDP_PRJ NC_000003.11 - 52431671 Apr 25, 2020 (154)
77 Siberian NC_000003.11 - 52431671 Apr 25, 2020 (154)
78 8.3KJPN NC_000003.11 - 52431671 Apr 26, 2021 (155)
79 TopMed NC_000003.12 - 52397655 Apr 26, 2021 (155)
80 UK 10K study - Twins NC_000003.11 - 52431671 Oct 12, 2018 (152)
81 A Vietnamese Genetic Variation Database NC_000003.11 - 52431671 Jul 13, 2019 (153)
82 ALFA NC_000003.12 - 52397655 Apr 26, 2021 (155)
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
ss111685553, ss117080693, ss202509454, ss277121969, ss1588052214, ss1712574790, ss3643371490 NC_000003.10:52406710:G:A NC_000003.12:52397654:G:A (self)
15155709, 8428032, 5960966, 6123657, 3695995, 8859849, 135382, 3163196, 216135, 3863336, 7844540, 2059660, 17096672, 8428032, 1830372, ss220132040, ss231817026, ss537207552, ss556608203, ss650286330, ss978581167, ss1070400372, ss1303968925, ss1429416713, ss1579958718, ss1607049897, ss1650043930, ss1711018843, ss1921821406, ss1969389597, ss2021469891, ss2149543306, ss2418582810, ss2704916329, ss2792877201, ss2992301286, ss3345013705, ss3628658591, ss3638414395, ss3646286644, ss3660222718, ss3729878331, ss3760021541, ss3825634334, ss3827803869, ss3855827560, ss3901682455, ss3984251432, ss3984251433, ss3984990208, ss3986240670, ss4017080397, ss5159127365 NC_000003.11:52431670:G:A NC_000003.12:52397654:G:A (self)
107598447, 2357538, 7630201, 251064840, 401806540, 6453105055, ss2251507653, ss3024496355, ss3390374559, ss3709214425, ss3803158738, ss3951252200, ss4564428985 NC_000003.12:52397654:G:A NC_000003.12:52397654:G:A (self)
ss505389, ss993901, ss1059956, ss1838025, ss1856256, ss44396218, ss75146187, ss119352470, ss173670328, ss410847287 NT_022517.18:52371670:G:A NC_000003.12:52397654: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.

2 citations for rs390802
PMID Title Author Year Journal
29088836 Common, germline genetic variations in the novel tumor suppressor <i>BAP1</i> and risk of developing different types of cancer. Lin M et al. 2017 Oncotarget
31637880 MicroRNA-binding site polymorphisms and risk of colorectal cancer: A systematic review and meta-analysis. Gholami M et al. 2019 Cancer 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.post596+ae089ad