Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

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.

rs17205642

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr5:83077008 (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=0.017492 (4630/264690, TOPMED)
A=0.019524 (2739/140286, GnomAD)
A=0.02270 (438/19292, ALFA) (+ 15 more)
A=0.0133 (85/6404, 1000G_30x)
A=0.0144 (72/5008, 1000G)
A=0.0272 (122/4480, Estonian)
A=0.0241 (93/3854, ALSPAC)
A=0.0227 (84/3708, TWINSUK)
A=0.0150 (17/1136, Daghestan)
A=0.017 (17/998, GoNL)
A=0.007 (4/600, NorthernSweden)
A=0.006 (2/326, HapMap)
A=0.019 (4/216, Qatari)
A=0.03 (1/40, GENOME_DK)
G=0.5 (4/8, SGDP_PRJ)
A=0.5 (4/8, SGDP_PRJ)
G=0.5 (1/2, Siberian)
A=0.5 (1/2, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
TMEM167A : Intron Variant
XRCC4 : 2KB Upstream 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 19292 G=0.97730 A=0.02270
European Sub 14370 G=0.97216 A=0.02784
African Sub 2974 G=0.9973 A=0.0027
African Others Sub 114 G=1.000 A=0.000
African American Sub 2860 G=0.9972 A=0.0028
Asian Sub 118 G=1.000 A=0.000
East Asian Sub 90 G=1.00 A=0.00
Other Asian Sub 28 G=1.00 A=0.00
Latin American 1 Sub 154 G=0.994 A=0.006
Latin American 2 Sub 616 G=0.989 A=0.011
South Asian Sub 100 G=0.98 A=0.02
Other Sub 960 G=0.979 A=0.021


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=0.982508 A=0.017492
gnomAD - Genomes Global Study-wide 140286 G=0.980476 A=0.019524
gnomAD - Genomes European Sub 75958 G=0.97296 A=0.02704
gnomAD - Genomes African Sub 42054 G=0.99548 A=0.00452
gnomAD - Genomes American Sub 13666 G=0.97834 A=0.02166
gnomAD - Genomes Ashkenazi Jewish Sub 3322 G=0.9491 A=0.0509
gnomAD - Genomes East Asian Sub 3134 G=0.9997 A=0.0003
gnomAD - Genomes Other Sub 2152 G=0.9865 A=0.0135
Allele Frequency Aggregator Total Global 19292 G=0.97730 A=0.02270
Allele Frequency Aggregator European Sub 14370 G=0.97216 A=0.02784
Allele Frequency Aggregator African Sub 2974 G=0.9973 A=0.0027
Allele Frequency Aggregator Other Sub 960 G=0.979 A=0.021
Allele Frequency Aggregator Latin American 2 Sub 616 G=0.989 A=0.011
Allele Frequency Aggregator Latin American 1 Sub 154 G=0.994 A=0.006
Allele Frequency Aggregator Asian Sub 118 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 100 G=0.98 A=0.02
1000Genomes_30x Global Study-wide 6404 G=0.9867 A=0.0133
1000Genomes_30x African Sub 1786 G=0.9989 A=0.0011
1000Genomes_30x Europe Sub 1266 G=0.9708 A=0.0292
1000Genomes_30x South Asian Sub 1202 G=0.9784 A=0.0216
1000Genomes_30x East Asian Sub 1170 G=1.0000 A=0.0000
1000Genomes_30x American Sub 980 G=0.980 A=0.020
1000Genomes Global Study-wide 5008 G=0.9856 A=0.0144
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=0.9692 A=0.0308
1000Genomes South Asian Sub 978 G=0.974 A=0.026
1000Genomes American Sub 694 G=0.978 A=0.022
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.9728 A=0.0272
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.9759 A=0.0241
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.9773 A=0.0227
Genome-wide autozygosity in Daghestan Global Study-wide 1136 G=0.9850 A=0.0150
Genome-wide autozygosity in Daghestan Daghestan Sub 628 G=0.986 A=0.014
Genome-wide autozygosity in Daghestan Near_East Sub 144 G=0.993 A=0.007
Genome-wide autozygosity in Daghestan Central Asia Sub 122 G=0.975 A=0.025
Genome-wide autozygosity in Daghestan Europe Sub 108 G=0.981 A=0.019
Genome-wide autozygosity in Daghestan South Asian Sub 98 G=0.99 A=0.01
Genome-wide autozygosity in Daghestan Caucasus Sub 36 G=0.97 A=0.03
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.983 A=0.017
Northern Sweden ACPOP Study-wide 600 G=0.993 A=0.007
HapMap Global Study-wide 326 G=0.994 A=0.006
HapMap African Sub 120 G=1.000 A=0.000
HapMap American Sub 118 G=0.983 A=0.017
HapMap Asian Sub 88 G=1.00 A=0.00
Qatari Global Study-wide 216 G=0.981 A=0.019
The Danish reference pan genome Danish Study-wide 40 G=0.97 A=0.03
SGDP_PRJ Global Study-wide 8 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 5 NC_000005.10:g.83077008G>A
GRCh37.p13 chr 5 NC_000005.9:g.82372827G>A
XRCC4 RefSeqGene NG_047086.1:g.4600G>A
Gene: TMEM167A, transmembrane protein 167A (minus strand)
Molecule type Change Amino acid[Codon] SO Term
TMEM167A transcript NM_174909.5:c.3+313C>T N/A Intron Variant
Gene: XRCC4, X-ray repair cross complementing 4 (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
XRCC4 transcript variant 4 NM_001318012.3:c. N/A Upstream Transcript Variant
XRCC4 transcript variant 5 NM_001318013.2:c. N/A Upstream Transcript Variant
XRCC4 transcript variant 1 NM_003401.5:c. N/A Upstream Transcript Variant
XRCC4 transcript variant 2 NM_022406.5:c. N/A Upstream Transcript Variant
XRCC4 transcript variant 3 NM_022550.4:c. N/A Upstream Transcript Variant
XRCC4 transcript variant X3 XM_017009827.3:c. N/A Upstream Transcript Variant
XRCC4 transcript variant X6 XM_017009828.3:c. N/A Upstream Transcript Variant
XRCC4 transcript variant X4 XM_047417695.1:c. N/A Upstream Transcript Variant
XRCC4 transcript variant X5 XM_047417696.1:c. N/A Upstream Transcript Variant
XRCC4 transcript variant X7 XM_047417697.1:c. N/A Upstream Transcript Variant
XRCC4 transcript variant X8 XM_047417698.1:c. N/A Upstream Transcript Variant
XRCC4 transcript variant X1 XM_011543626.2:c. N/A N/A
XRCC4 transcript variant X2 XM_047417694.1:c. N/A N/A
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
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 5 NC_000005.10:g.83077008= NC_000005.10:g.83077008G>A
GRCh37.p13 chr 5 NC_000005.9:g.82372827= NC_000005.9:g.82372827G>A
XRCC4 RefSeqGene NG_047086.1:g.4600= NG_047086.1:g.4600G>A
TMEM167A transcript NM_174909.4:c.3+313= NM_174909.4:c.3+313C>T
TMEM167A transcript NM_174909.5:c.3+313= NM_174909.5:c.3+313C>T
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, 16 Frequency submissions
No Submitter Submission ID Date (Build)
1 PERLEGEN ss24621074 Sep 20, 2004 (123)
2 EGP_SNPS ss35039628 May 24, 2005 (125)
3 BCM-HGSC-SUB ss206793517 Jul 04, 2010 (132)
4 1000GENOMES ss332585686 May 09, 2011 (134)
5 ILLUMINA ss535416539 Sep 08, 2015 (146)
6 EVA-GONL ss981757049 Aug 21, 2014 (142)
7 1000GENOMES ss1315820011 Aug 21, 2014 (142)
8 HAMMER_LAB ss1397418494 Sep 08, 2015 (146)
9 EVA_GENOME_DK ss1581211536 Apr 01, 2015 (144)
10 EVA_DECODE ss1591275368 Apr 01, 2015 (144)
11 EVA_UK10K_ALSPAC ss1613271075 Apr 01, 2015 (144)
12 EVA_UK10K_TWINSUK ss1656265108 Apr 01, 2015 (144)
13 WEILL_CORNELL_DGM ss1925011817 Feb 12, 2016 (147)
14 JJLAB ss2023112707 Sep 14, 2016 (149)
15 USC_VALOUEV ss2151268904 Dec 20, 2016 (150)
16 HUMAN_LONGEVITY ss2275200732 Dec 20, 2016 (150)
17 GNOMAD ss2826731778 Nov 08, 2017 (151)
18 SWEGEN ss2997234553 Nov 08, 2017 (151)
19 ILLUMINA ss3022503480 Nov 08, 2017 (151)
20 ILLUMINA ss3625876825 Oct 12, 2018 (152)
21 ILLUMINA ss3629273689 Oct 12, 2018 (152)
22 ILLUMINA ss3653000454 Oct 12, 2018 (152)
23 EGCUT_WGS ss3665114099 Jul 13, 2019 (153)
24 EVA_DECODE ss3715035794 Jul 13, 2019 (153)
25 ILLUMINA ss3726246409 Jul 13, 2019 (153)
26 ACPOP ss3732514486 Jul 13, 2019 (153)
27 EVA ss3763648644 Jul 13, 2019 (153)
28 KHV_HUMAN_GENOMES ss3806815728 Jul 13, 2019 (153)
29 EVA ss3829335039 Apr 26, 2020 (154)
30 SGDP_PRJ ss3862245654 Apr 26, 2020 (154)
31 TOPMED ss4666300831 Apr 26, 2021 (155)
32 EVA ss5237374411 Apr 26, 2021 (155)
33 1000G_HIGH_COVERAGE ss5264618933 Oct 13, 2022 (156)
34 EVA ss5358734313 Oct 13, 2022 (156)
35 HUGCELL_USP ss5462725356 Oct 13, 2022 (156)
36 1000G_HIGH_COVERAGE ss5548597168 Oct 13, 2022 (156)
37 SANFORD_IMAGENETICS ss5624593691 Oct 13, 2022 (156)
38 SANFORD_IMAGENETICS ss5638172960 Oct 13, 2022 (156)
39 EVA ss5835175555 Oct 13, 2022 (156)
40 EVA ss5847269294 Oct 13, 2022 (156)
41 EVA ss5848055118 Oct 13, 2022 (156)
42 EVA ss5894913066 Oct 13, 2022 (156)
43 EVA ss5966608130 Oct 13, 2022 (156)
44 EVA ss5979745068 Oct 13, 2022 (156)
45 1000Genomes NC_000005.9 - 82372827 Oct 12, 2018 (152)
46 1000Genomes_30x NC_000005.10 - 83077008 Oct 13, 2022 (156)
47 The Avon Longitudinal Study of Parents and Children NC_000005.9 - 82372827 Oct 12, 2018 (152)
48 Genome-wide autozygosity in Daghestan NC_000005.8 - 82408583 Apr 26, 2020 (154)
49 Genetic variation in the Estonian population NC_000005.9 - 82372827 Oct 12, 2018 (152)
50 The Danish reference pan genome NC_000005.9 - 82372827 Apr 26, 2020 (154)
51 gnomAD - Genomes NC_000005.10 - 83077008 Apr 26, 2021 (155)
52 Genome of the Netherlands Release 5 NC_000005.9 - 82372827 Apr 26, 2020 (154)
53 HapMap NC_000005.10 - 83077008 Apr 26, 2020 (154)
54 Northern Sweden NC_000005.9 - 82372827 Jul 13, 2019 (153)
55 Qatari NC_000005.9 - 82372827 Apr 26, 2020 (154)
56 SGDP_PRJ NC_000005.9 - 82372827 Apr 26, 2020 (154)
57 Siberian NC_000005.9 - 82372827 Apr 26, 2020 (154)
58 TopMed NC_000005.10 - 83077008 Apr 26, 2021 (155)
59 UK 10K study - Twins NC_000005.9 - 82372827 Oct 12, 2018 (152)
60 ALFA NC_000005.10 - 83077008 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
393465, ss206793517, ss1397418494, ss1591275368 NC_000005.8:82408582:G:A NC_000005.10:83077007:G:A (self)
27447214, 15261540, 10852347, 7376475, 6784903, 5799351, 7053747, 14262634, 3785258, 15261540, ss332585686, ss535416539, ss981757049, ss1315820011, ss1581211536, ss1613271075, ss1656265108, ss1925011817, ss2023112707, ss2151268904, ss2826731778, ss2997234553, ss3022503480, ss3625876825, ss3629273689, ss3653000454, ss3665114099, ss3732514486, ss3763648644, ss3829335039, ss3862245654, ss5237374411, ss5358734313, ss5624593691, ss5638172960, ss5835175555, ss5847269294, ss5848055118, ss5966608130, ss5979745068 NC_000005.9:82372826:G:A NC_000005.10:83077007:G:A (self)
36123103, 194028913, 2902296, 503678388, 3858093152, ss2275200732, ss3715035794, ss3726246409, ss3806815728, ss4666300831, ss5264618933, ss5462725356, ss5548597168, ss5894913066 NC_000005.10:83077007:G:A NC_000005.10:83077007:G:A (self)
ss24621074, ss35039628 NT_006713.15:32967185:G:A NC_000005.10:83077007: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 rs17205642

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