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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.

rs1039430

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr5:35150933 (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
A>C / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.225974 (59813/264690, TOPMED)
A=0.215446 (30175/140058, GnomAD)
A=0.19354 (5469/28258, 14KJPN) (+ 15 more)
A=0.15738 (2973/18890, ALFA)
A=0.19409 (3253/16760, 8.3KJPN)
A=0.2431 (1557/6404, 1000G_30x)
A=0.2352 (1178/5008, 1000G)
A=0.0895 (401/4480, Estonian)
A=0.0784 (302/3854, ALSPAC)
A=0.0785 (291/3708, TWINSUK)
A=0.2157 (632/2930, KOREAN)
A=0.071 (71/998, GoNL)
A=0.110 (66/600, NorthernSweden)
A=0.126 (63/500, SGDP_PRJ)
A=0.245 (53/216, Qatari)
A=0.167 (36/216, Vietnamese)
A=0.05 (3/56, Siberian)
A=0.07 (3/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
PRLR : Intron 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 18890 A=0.15738 T=0.84262
European Sub 14286 A=0.08743 T=0.91257
African Sub 2946 A=0.5007 T=0.4993
African Others Sub 114 A=0.553 T=0.447
African American Sub 2832 A=0.4986 T=0.5014
Asian Sub 112 A=0.223 T=0.777
East Asian Sub 86 A=0.21 T=0.79
Other Asian Sub 26 A=0.27 T=0.73
Latin American 1 Sub 146 A=0.219 T=0.781
Latin American 2 Sub 610 A=0.095 T=0.905
South Asian Sub 98 A=0.09 T=0.91
Other Sub 692 A=0.181 T=0.819


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 A=0.225974 T=0.774026
gnomAD - Genomes Global Study-wide 140058 A=0.215446 T=0.784554
gnomAD - Genomes European Sub 75912 A=0.08187 T=0.91813
gnomAD - Genomes African Sub 41914 A=0.49711 T=0.50289
gnomAD - Genomes American Sub 13636 A=0.12584 T=0.87416
gnomAD - Genomes Ashkenazi Jewish Sub 3322 A=0.1123 T=0.8877
gnomAD - Genomes East Asian Sub 3124 A=0.1985 T=0.8015
gnomAD - Genomes Other Sub 2150 A=0.1930 T=0.8070
14KJPN JAPANESE Study-wide 28258 A=0.19354 T=0.80646
Allele Frequency Aggregator Total Global 18890 A=0.15738 T=0.84262
Allele Frequency Aggregator European Sub 14286 A=0.08743 T=0.91257
Allele Frequency Aggregator African Sub 2946 A=0.5007 T=0.4993
Allele Frequency Aggregator Other Sub 692 A=0.181 T=0.819
Allele Frequency Aggregator Latin American 2 Sub 610 A=0.095 T=0.905
Allele Frequency Aggregator Latin American 1 Sub 146 A=0.219 T=0.781
Allele Frequency Aggregator Asian Sub 112 A=0.223 T=0.777
Allele Frequency Aggregator South Asian Sub 98 A=0.09 T=0.91
8.3KJPN JAPANESE Study-wide 16760 A=0.19409 T=0.80591
1000Genomes_30x Global Study-wide 6404 A=0.2431 T=0.7569
1000Genomes_30x African Sub 1786 A=0.5756 T=0.4244
1000Genomes_30x Europe Sub 1266 A=0.0798 T=0.9202
1000Genomes_30x South Asian Sub 1202 A=0.1015 T=0.8985
1000Genomes_30x East Asian Sub 1170 A=0.1726 T=0.8274
1000Genomes_30x American Sub 980 A=0.106 T=0.894
1000Genomes Global Study-wide 5008 A=0.2352 T=0.7648
1000Genomes African Sub 1322 A=0.5605 T=0.4395
1000Genomes East Asian Sub 1008 A=0.1726 T=0.8274
1000Genomes Europe Sub 1006 A=0.0825 T=0.9175
1000Genomes South Asian Sub 978 A=0.107 T=0.893
1000Genomes American Sub 694 A=0.108 T=0.892
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.0895 T=0.9105
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.0784 T=0.9216
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.0785 T=0.9215
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.2157 C=0.0000, T=0.7843
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.071 T=0.929
Northern Sweden ACPOP Study-wide 600 A=0.110 T=0.890
SGDP_PRJ Global Study-wide 500 A=0.126 T=0.874
Qatari Global Study-wide 216 A=0.245 T=0.755
A Vietnamese Genetic Variation Database Global Study-wide 216 A=0.167 T=0.833
Siberian Global Study-wide 56 A=0.05 T=0.95
The Danish reference pan genome Danish Study-wide 40 A=0.07 T=0.93
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.35150933A>C
GRCh38.p14 chr 5 NC_000005.10:g.35150933A>T
GRCh37.p13 chr 5 NC_000005.9:g.35151035A>C
GRCh37.p13 chr 5 NC_000005.9:g.35151035A>T
PRLR RefSeqGene NG_029042.2:g.84789T>G
PRLR RefSeqGene NG_029042.2:g.84789T>A
Gene: PRLR, prolactin receptor (minus strand)
Molecule type Change Amino acid[Codon] SO Term
PRLR transcript variant 1 NM_000949.7:c.-105-32811T…

NM_000949.7:c.-105-32811T>G

N/A Intron Variant
PRLR transcript variant 6 NM_001204314.2:c. N/A Genic Upstream Transcript Variant
PRLR transcript variant 2 NM_001204315.1:c. N/A Genic Upstream Transcript Variant
PRLR transcript variant 3 NM_001204316.1:c. N/A Genic Upstream Transcript Variant
PRLR transcript variant 4 NM_001204317.1:c. N/A Genic Upstream Transcript Variant
PRLR transcript variant 5 NM_001204318.1:c. N/A Genic Upstream Transcript Variant
PRLR transcript variant 7 NR_037910.1:n. N/A Genic Upstream Transcript Variant
PRLR transcript variant X3 XM_006714484.3:c.-105-328…

XM_006714484.3:c.-105-32811T>G

N/A Intron Variant
PRLR transcript variant X4 XM_011514068.3:c.-199-155…

XM_011514068.3:c.-199-15543T>G

N/A Intron Variant
PRLR transcript variant X1 XM_024446131.2:c.60-61270…

XM_024446131.2:c.60-61270T>G

N/A Intron Variant
PRLR transcript variant X2 XM_047417388.1:c.-105-328…

XM_047417388.1:c.-105-32811T>G

N/A Intron Variant
PRLR transcript variant X5 XM_047417390.1:c.-106+185…

XM_047417390.1:c.-106+1854T>G

N/A Intron Variant
PRLR transcript variant X6 XM_047417391.1:c. N/A Genic Upstream Transcript 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
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 A= C T
GRCh38.p14 chr 5 NC_000005.10:g.35150933= NC_000005.10:g.35150933A>C NC_000005.10:g.35150933A>T
GRCh37.p13 chr 5 NC_000005.9:g.35151035= NC_000005.9:g.35151035A>C NC_000005.9:g.35151035A>T
PRLR RefSeqGene NG_029042.2:g.84789= NG_029042.2:g.84789T>G NG_029042.2:g.84789T>A
PRLR transcript variant 1 NM_000949.5:c.-105-32811= NM_000949.5:c.-105-32811T>G NM_000949.5:c.-105-32811T>A
PRLR transcript variant 1 NM_000949.7:c.-105-32811= NM_000949.7:c.-105-32811T>G NM_000949.7:c.-105-32811T>A
PRLR transcript variant X3 XM_006714484.3:c.-105-32811= XM_006714484.3:c.-105-32811T>G XM_006714484.3:c.-105-32811T>A
PRLR transcript variant X4 XM_011514068.3:c.-199-15543= XM_011514068.3:c.-199-15543T>G XM_011514068.3:c.-199-15543T>A
PRLR transcript variant X1 XM_024446131.2:c.60-61270= XM_024446131.2:c.60-61270T>G XM_024446131.2:c.60-61270T>A
PRLR transcript variant X2 XM_047417388.1:c.-105-32811= XM_047417388.1:c.-105-32811T>G XM_047417388.1:c.-105-32811T>A
PRLR transcript variant X5 XM_047417390.1:c.-106+1854= XM_047417390.1:c.-106+1854T>G XM_047417390.1:c.-106+1854T>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#.

81 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss1505786 Oct 05, 2000 (86)
2 TSC-CSHL ss5493346 Oct 10, 2002 (110)
3 WI_SSAHASNP ss14638182 Dec 05, 2003 (119)
4 CSHL-HAPMAP ss17072633 Feb 27, 2004 (120)
5 CSHL-HAPMAP ss17847628 Feb 27, 2004 (120)
6 CSHL-HAPMAP ss19629479 Feb 27, 2004 (120)
7 SSAHASNP ss22217990 Apr 05, 2004 (121)
8 PERLEGEN ss23747949 Sep 20, 2004 (123)
9 ABI ss44620142 Mar 13, 2006 (126)
10 HGSV ss77402493 Dec 06, 2007 (129)
11 HGSV ss78287609 Dec 06, 2007 (129)
12 BCMHGSC_JDW ss93058637 Mar 24, 2008 (129)
13 HUMANGENOME_JCVI ss98713117 Feb 06, 2009 (130)
14 BGI ss105919026 Feb 06, 2009 (130)
15 1000GENOMES ss108954479 Jan 23, 2009 (130)
16 1000GENOMES ss111686394 Jan 25, 2009 (130)
17 ILLUMINA-UK ss116565208 Feb 14, 2009 (130)
18 ENSEMBL ss143029446 Dec 01, 2009 (131)
19 ENSEMBL ss144174683 Dec 01, 2009 (131)
20 GMI ss155294515 Dec 01, 2009 (131)
21 COMPLETE_GENOMICS ss162168511 Jul 04, 2010 (132)
22 COMPLETE_GENOMICS ss164690729 Jul 04, 2010 (132)
23 COMPLETE_GENOMICS ss166411023 Jul 04, 2010 (132)
24 BUSHMAN ss200107145 Jul 04, 2010 (132)
25 BCM-HGSC-SUB ss206776109 Jul 04, 2010 (132)
26 1000GENOMES ss221620199 Jul 14, 2010 (132)
27 1000GENOMES ss232901881 Jul 14, 2010 (132)
28 1000GENOMES ss240084873 Jul 15, 2010 (132)
29 BL ss253368951 May 09, 2011 (134)
30 GMI ss278243349 May 04, 2012 (137)
31 GMI ss285155550 Apr 25, 2013 (138)
32 PJP ss293566944 May 09, 2011 (134)
33 TISHKOFF ss558319996 Apr 25, 2013 (138)
34 EVA-GONL ss981439283 Aug 21, 2014 (142)
35 JMKIDD_LAB ss1072536574 Aug 21, 2014 (142)
36 1000GENOMES ss1314615589 Aug 21, 2014 (142)
37 DDI ss1430306391 Apr 01, 2015 (144)
38 EVA_GENOME_DK ss1581090742 Apr 01, 2015 (144)
39 EVA_DECODE ss1590961505 Apr 01, 2015 (144)
40 EVA_UK10K_ALSPAC ss1612640872 Apr 01, 2015 (144)
41 EVA_UK10K_TWINSUK ss1655634905 Apr 01, 2015 (144)
42 HAMMER_LAB ss1803350507 Sep 08, 2015 (146)
43 WEILL_CORNELL_DGM ss1924702116 Feb 12, 2016 (147)
44 GENOMED ss1970062001 Jul 19, 2016 (147)
45 JJLAB ss2022953798 Sep 14, 2016 (149)
46 USC_VALOUEV ss2151104523 Dec 20, 2016 (150)
47 HUMAN_LONGEVITY ss2272810838 Dec 20, 2016 (150)
48 SYSTEMSBIOZJU ss2625977425 Nov 08, 2017 (151)
49 GRF ss2706640818 Nov 08, 2017 (151)
50 GNOMAD ss2823182822 Nov 08, 2017 (151)
51 SWEGEN ss2996728877 Nov 08, 2017 (151)
52 BIOINF_KMB_FNS_UNIBA ss3025262280 Nov 08, 2017 (151)
53 CSHL ss3346332616 Nov 08, 2017 (151)
54 URBANLAB ss3648031461 Oct 12, 2018 (152)
55 EGCUT_WGS ss3664621602 Jul 13, 2019 (153)
56 EVA_DECODE ss3714456672 Jul 13, 2019 (153)
57 ACPOP ss3732252414 Jul 13, 2019 (153)
58 EVA ss3763286436 Jul 13, 2019 (153)
59 PACBIO ss3785080267 Jul 13, 2019 (153)
60 PACBIO ss3790491561 Jul 13, 2019 (153)
61 PACBIO ss3795367991 Jul 13, 2019 (153)
62 KHV_HUMAN_GENOMES ss3806462102 Jul 13, 2019 (153)
63 EVA ss3829189759 Apr 26, 2020 (154)
64 EVA ss3838064092 Apr 26, 2020 (154)
65 EVA ss3843503323 Apr 26, 2020 (154)
66 SGDP_PRJ ss3861602103 Apr 26, 2020 (154)
67 KRGDB ss3908074126 Apr 26, 2020 (154)
68 TOPMED ss4655705912 Apr 26, 2021 (155)
69 TOMMO_GENOMICS ss5171189345 Apr 26, 2021 (155)
70 1000G_HIGH_COVERAGE ss5263515494 Oct 13, 2022 (156)
71 EVA ss5356796412 Oct 13, 2022 (156)
72 HUGCELL_USP ss5461787579 Oct 13, 2022 (156)
73 EVA ss5507977617 Oct 13, 2022 (156)
74 1000G_HIGH_COVERAGE ss5546911617 Oct 13, 2022 (156)
75 SANFORD_IMAGENETICS ss5637561275 Oct 13, 2022 (156)
76 TOMMO_GENOMICS ss5707083068 Oct 13, 2022 (156)
77 YY_MCH ss5806181960 Oct 13, 2022 (156)
78 EVA ss5834769557 Oct 13, 2022 (156)
79 EVA ss5854765468 Oct 13, 2022 (156)
80 EVA ss5893703749 Oct 13, 2022 (156)
81 EVA ss5965976306 Oct 13, 2022 (156)
82 1000Genomes NC_000005.9 - 35151035 Oct 12, 2018 (152)
83 1000Genomes_30x NC_000005.10 - 35150933 Oct 13, 2022 (156)
84 The Avon Longitudinal Study of Parents and Children NC_000005.9 - 35151035 Oct 12, 2018 (152)
85 Genetic variation in the Estonian population NC_000005.9 - 35151035 Oct 12, 2018 (152)
86 The Danish reference pan genome NC_000005.9 - 35151035 Apr 26, 2020 (154)
87 gnomAD - Genomes NC_000005.10 - 35150933 Apr 26, 2021 (155)
88 Genome of the Netherlands Release 5 NC_000005.9 - 35151035 Apr 26, 2020 (154)
89 KOREAN population from KRGDB NC_000005.9 - 35151035 Apr 26, 2020 (154)
90 Northern Sweden NC_000005.9 - 35151035 Jul 13, 2019 (153)
91 Qatari NC_000005.9 - 35151035 Apr 26, 2020 (154)
92 SGDP_PRJ NC_000005.9 - 35151035 Apr 26, 2020 (154)
93 Siberian NC_000005.9 - 35151035 Apr 26, 2020 (154)
94 8.3KJPN NC_000005.9 - 35151035 Apr 26, 2021 (155)
95 14KJPN NC_000005.10 - 35150933 Oct 13, 2022 (156)
96 TopMed NC_000005.10 - 35150933 Apr 26, 2021 (155)
97 UK 10K study - Twins NC_000005.9 - 35151035 Oct 12, 2018 (152)
98 A Vietnamese Genetic Variation Database NC_000005.9 - 35151035 Jul 13, 2019 (153)
99 ALFA NC_000005.10 - 35150933 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).

Associated ID History Updated (Build)
rs4089156 Dec 16, 2002 (110)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
15251520, ss3908074126 NC_000005.9:35151034:A:C NC_000005.10:35150932:A:C (self)
ss77402493, ss78287609, ss93058637, ss108954479, ss111686394, ss116565208, ss162168511, ss164690729, ss166411023, ss200107145, ss206776109, ss253368951, ss278243349, ss285155550, ss293566944, ss1590961505 NC_000005.8:35186791:A:T NC_000005.10:35150932:A:T (self)
26199015, 14569954, 10359850, 7255681, 6475296, 15251520, 5537279, 6744046, 13619083, 3620877, 29158652, 14569954, 3239222, ss221620199, ss232901881, ss240084873, ss558319996, ss981439283, ss1072536574, ss1314615589, ss1430306391, ss1581090742, ss1612640872, ss1655634905, ss1803350507, ss1924702116, ss1970062001, ss2022953798, ss2151104523, ss2625977425, ss2706640818, ss2823182822, ss2996728877, ss3346332616, ss3664621602, ss3732252414, ss3763286436, ss3785080267, ss3790491561, ss3795367991, ss3829189759, ss3838064092, ss3861602103, ss3908074126, ss5171189345, ss5356796412, ss5507977617, ss5637561275, ss5834769557, ss5965976306 NC_000005.9:35151034:A:T NC_000005.10:35150932:A:T (self)
34437552, 185088776, 40920172, 493083469, 2722895862, ss2272810838, ss3025262280, ss3648031461, ss3714456672, ss3806462102, ss3843503323, ss4655705912, ss5263515494, ss5461787579, ss5546911617, ss5707083068, ss5806181960, ss5854765468, ss5893703749 NC_000005.10:35150932:A:T NC_000005.10:35150932:A:T (self)
ss14638182, ss17072633, ss17847628, ss19629479, ss22217990 NT_006576.14:17603140:A:T NC_000005.10:35150932:A:T (self)
ss1505786, ss5493346, ss23747949, ss44620142, ss98713117, ss105919026, ss143029446, ss144174683, ss155294515 NT_006576.16:35141034:A:T NC_000005.10:35150932:A: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 rs1039430

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