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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.

rs73990423

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr2:218340131 (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>C
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.019566 (5179/264690, TOPMED)
A=0.004285 (1074/250638, GnomAD_exome)
A=0.001056 (222/210184, ALFA) (+ 9 more)
A=0.018253 (2553/139866, GnomAD)
A=0.005243 (630/120162, ExAC)
A=0.02977 (2343/78696, PAGE_STUDY)
A=0.01907 (248/13006, GO-ESP)
A=0.0201 (129/6404, 1000G_30x)
A=0.0180 (90/5008, 1000G)
A=0.005 (1/216, Qatari)
G=0.5 (3/6, SGDP_PRJ)
A=0.5 (3/6, SGDP_PRJ)
Clinical Significance
Reported in ClinVar
Gene : Consequence
PNKD : Missense Variant
CATIP-AS2 : Intron Variant
MIR6810 : 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 210306 G=0.998940 A=0.001060, C=0.000000
European Sub 180396 G=0.999828 A=0.000172, C=0.000000
African Sub 4944 G=0.9709 A=0.0291, C=0.0000
African Others Sub 174 G=0.971 A=0.029, C=0.000
African American Sub 4770 G=0.9709 A=0.0291, C=0.0000
Asian Sub 6364 G=0.9998 A=0.0002, C=0.0000
East Asian Sub 4514 G=0.9998 A=0.0002, C=0.0000
Other Asian Sub 1850 G=1.0000 A=0.0000, C=0.0000
Latin American 1 Sub 796 G=0.986 A=0.014, C=0.000
Latin American 2 Sub 1052 G=0.9990 A=0.0010, C=0.0000
South Asian Sub 296 G=1.000 A=0.000, C=0.000
Other Sub 16458 G=0.99787 A=0.00213, C=0.00000


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=0.980434 A=0.019566
gnomAD - Exomes Global Study-wide 250638 G=0.995715 A=0.004285
gnomAD - Exomes European Sub 134750 G=0.999844 A=0.000156
gnomAD - Exomes Asian Sub 48980 G=0.99990 A=0.00010
gnomAD - Exomes American Sub 34560 G=0.99719 A=0.00281
gnomAD - Exomes African Sub 16172 G=0.94212 A=0.05788
gnomAD - Exomes Ashkenazi Jewish Sub 10060 G=1.00000 A=0.00000
gnomAD - Exomes Other Sub 6116 G=0.9975 A=0.0025
Allele Frequency Aggregator Total Global 210184 G=0.998944 A=0.001056, C=0.000000
Allele Frequency Aggregator European Sub 180292 G=0.999828 A=0.000172, C=0.000000
Allele Frequency Aggregator Other Sub 16454 G=0.99787 A=0.00213, C=0.00000
Allele Frequency Aggregator Asian Sub 6364 G=0.9998 A=0.0002, C=0.0000
Allele Frequency Aggregator African Sub 4930 G=0.9710 A=0.0290, C=0.0000
Allele Frequency Aggregator Latin American 2 Sub 1052 G=0.9990 A=0.0010, C=0.0000
Allele Frequency Aggregator Latin American 1 Sub 796 G=0.986 A=0.014, C=0.000
Allele Frequency Aggregator South Asian Sub 296 G=1.000 A=0.000, C=0.000
gnomAD - Genomes Global Study-wide 139866 G=0.981747 A=0.018253
gnomAD - Genomes European Sub 75804 G=0.99980 A=0.00020
gnomAD - Genomes African Sub 41844 G=0.94226 A=0.05774
gnomAD - Genomes American Sub 13626 G=0.99325 A=0.00675
gnomAD - Genomes Ashkenazi Jewish Sub 3320 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3124 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2148 G=0.9860 A=0.0140
ExAC Global Study-wide 120162 G=0.994757 A=0.005243
ExAC Europe Sub 72414 G=0.99979 A=0.00021
ExAC Asian Sub 25076 G=0.99996 A=0.00004
ExAC American Sub 11544 G=0.99757 A=0.00243
ExAC African Sub 10238 G=0.94335 A=0.05665
ExAC Other Sub 890 G=0.993 A=0.007
The PAGE Study Global Study-wide 78696 G=0.97023 A=0.02977
The PAGE Study AfricanAmerican Sub 32512 G=0.94171 A=0.05829
The PAGE Study Mexican Sub 10810 G=0.99713 A=0.00287
The PAGE Study Asian Sub 8318 G=1.0000 A=0.0000
The PAGE Study PuertoRican Sub 7918 G=0.9795 A=0.0205
The PAGE Study NativeHawaiian Sub 4534 G=0.9991 A=0.0009
The PAGE Study Cuban Sub 4230 G=0.9853 A=0.0147
The PAGE Study Dominican Sub 3828 G=0.9660 A=0.0340
The PAGE Study CentralAmerican Sub 2450 G=0.9865 A=0.0135
The PAGE Study SouthAmerican Sub 1982 G=0.9934 A=0.0066
The PAGE Study NativeAmerican Sub 1260 G=0.9897 A=0.0103
The PAGE Study SouthAsian Sub 854 G=1.000 A=0.000
GO Exome Sequencing Project Global Study-wide 13006 G=0.98093 A=0.01907
GO Exome Sequencing Project European American Sub 8600 G=0.9997 A=0.0003
GO Exome Sequencing Project African American Sub 4406 G=0.9444 A=0.0556
1000Genomes_30x Global Study-wide 6404 G=0.9799 A=0.0201
1000Genomes_30x African Sub 1786 G=0.9300 A=0.0700
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=0.996 A=0.004
1000Genomes Global Study-wide 5008 G=0.9820 A=0.0180
1000Genomes African Sub 1322 G=0.9342 A=0.0658
1000Genomes East Asian Sub 1008 G=1.0000 A=0.0000
1000Genomes Europe Sub 1006 G=1.0000 A=0.0000
1000Genomes South Asian Sub 978 G=1.000 A=0.000
1000Genomes American Sub 694 G=0.996 A=0.004
Qatari Global Study-wide 216 G=0.995 A=0.005
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 2 NC_000002.12:g.218340131G>A
GRCh38.p14 chr 2 NC_000002.12:g.218340131G>C
GRCh37.p13 chr 2 NC_000002.11:g.219204854G>A
GRCh37.p13 chr 2 NC_000002.11:g.219204854G>C
PNKD RefSeqGene NG_017060.1:g.74740G>A
PNKD RefSeqGene NG_017060.1:g.74740G>C
Gene: PNKD, PNKD metallo-beta-lactamase domain containing (plus strand)
Molecule type Change Amino acid[Codon] SO Term
PNKD transcript variant 3 NM_001077399.3:c. N/A Genic Downstream Transcript Variant
PNKD transcript variant 2 NM_022572.4:c.383G>A R [CGG] > Q [CAG] Coding Sequence Variant
probable hydrolase PNKD isoform 2 NP_072094.1:p.Arg128Gln R (Arg) > Q (Gln) Missense Variant
PNKD transcript variant 2 NM_022572.4:c.383G>C R [CGG] > P [CCG] Coding Sequence Variant
probable hydrolase PNKD isoform 2 NP_072094.1:p.Arg128Pro R (Arg) > P (Pro) Missense Variant
PNKD transcript variant 1 NM_015488.5:c.455G>A R [CGG] > Q [CAG] Coding Sequence Variant
probable hydrolase PNKD isoform 1 precursor NP_056303.3:p.Arg152Gln R (Arg) > Q (Gln) Missense Variant
PNKD transcript variant 1 NM_015488.5:c.455G>C R [CGG] > P [CCG] Coding Sequence Variant
probable hydrolase PNKD isoform 1 precursor NP_056303.3:p.Arg152Pro R (Arg) > P (Pro) Missense Variant
PNKD transcript variant X1 XM_017003771.2:c.455G>A R [CGG] > Q [CAG] Coding Sequence Variant
probable hydrolase PNKD isoform X1 XP_016859260.1:p.Arg152Gln R (Arg) > Q (Gln) Missense Variant
PNKD transcript variant X1 XM_017003771.2:c.455G>C R [CGG] > P [CCG] Coding Sequence Variant
probable hydrolase PNKD isoform X1 XP_016859260.1:p.Arg152Pro R (Arg) > P (Pro) Missense Variant
PNKD transcript variant X2 XM_017003772.2:c.383G>A R [CGG] > Q [CAG] Coding Sequence Variant
probable hydrolase PNKD isoform X2 XP_016859261.1:p.Arg128Gln R (Arg) > Q (Gln) Missense Variant
PNKD transcript variant X2 XM_017003772.2:c.383G>C R [CGG] > P [CCG] Coding Sequence Variant
probable hydrolase PNKD isoform X2 XP_016859261.1:p.Arg128Pro R (Arg) > P (Pro) Missense Variant
Gene: CATIP-AS2, CATIP antisense RNA 2 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
CATIP-AS2 transcript NR_125777.1:n. N/A Intron Variant
Gene: MIR6810, microRNA 6810 (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
MIR6810 transcript NR_106868.1:n. N/A 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.

Allele: A (allele ID: 285345 )
ClinVar Accession Disease Names Clinical Significance
RCV000272595.8 Paroxysmal nonkinesigenic dyskinesia 1 Benign
RCV000857916.6 Paroxysmal nonkinesigenic dyskinesia Benign
RCV001598655.3 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 C
GRCh38.p14 chr 2 NC_000002.12:g.218340131= NC_000002.12:g.218340131G>A NC_000002.12:g.218340131G>C
GRCh37.p13 chr 2 NC_000002.11:g.219204854= NC_000002.11:g.219204854G>A NC_000002.11:g.219204854G>C
PNKD RefSeqGene NG_017060.1:g.74740= NG_017060.1:g.74740G>A NG_017060.1:g.74740G>C
PNKD transcript variant 1 NM_015488.5:c.455= NM_015488.5:c.455G>A NM_015488.5:c.455G>C
PNKD transcript variant 1 NM_015488.4:c.455= NM_015488.4:c.455G>A NM_015488.4:c.455G>C
PNKD transcript variant 2 NM_022572.4:c.383= NM_022572.4:c.383G>A NM_022572.4:c.383G>C
PNKD transcript variant X2 XM_017003772.2:c.383= XM_017003772.2:c.383G>A XM_017003772.2:c.383G>C
PNKD transcript variant X2 XM_017003772.1:c.383= XM_017003772.1:c.383G>A XM_017003772.1:c.383G>C
PNKD transcript variant X1 XM_017003771.2:c.455= XM_017003771.2:c.455G>A XM_017003771.2:c.455G>C
PNKD transcript variant X1 XM_017003771.1:c.455= XM_017003771.1:c.455G>A XM_017003771.1:c.455G>C
probable hydrolase PNKD isoform 1 precursor NP_056303.3:p.Arg152= NP_056303.3:p.Arg152Gln NP_056303.3:p.Arg152Pro
probable hydrolase PNKD isoform 2 NP_072094.1:p.Arg128= NP_072094.1:p.Arg128Gln NP_072094.1:p.Arg128Pro
probable hydrolase PNKD isoform X2 XP_016859261.1:p.Arg128= XP_016859261.1:p.Arg128Gln XP_016859261.1:p.Arg128Pro
probable hydrolase PNKD isoform X1 XP_016859260.1:p.Arg152= XP_016859260.1:p.Arg152Gln XP_016859260.1:p.Arg152Pro
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#.

56 SubSNP, 11 Frequency, 3 ClinVar submissions
No Submitter Submission ID Date (Build)
1 ILLUMINA-UK ss118082290 Feb 14, 2009 (130)
2 SEATTLESEQ ss159703675 Dec 01, 2009 (131)
3 BUSHMAN ss201754564 Jul 04, 2010 (132)
4 1000GENOMES ss219819760 Jul 14, 2010 (132)
5 NHLBI-ESP ss342098321 May 09, 2011 (134)
6 ILLUMINA ss480591584 May 04, 2012 (137)
7 ILLUMINA ss484015482 May 04, 2012 (137)
8 1000GENOMES ss489851640 May 04, 2012 (137)
9 EXOME_CHIP ss491331150 May 04, 2012 (137)
10 ILLUMINA ss533831645 Sep 08, 2015 (146)
11 TISHKOFF ss556227671 Apr 25, 2013 (138)
12 ILLUMINA ss779085178 Sep 08, 2015 (146)
13 ILLUMINA ss780810239 Sep 08, 2015 (146)
14 ILLUMINA ss781269194 Sep 08, 2015 (146)
15 ILLUMINA ss783492048 Sep 08, 2015 (146)
16 ILLUMINA ss834548970 Sep 08, 2015 (146)
17 1000GENOMES ss1301692879 Aug 21, 2014 (142)
18 EVA_EXAC ss1686728666 Apr 01, 2015 (144)
19 ILLUMINA ss1752339094 Sep 08, 2015 (146)
20 ILLUMINA ss1917759716 Feb 12, 2016 (147)
21 WEILL_CORNELL_DGM ss1921218018 Feb 12, 2016 (147)
22 ILLUMINA ss1946066455 Feb 12, 2016 (147)
23 ILLUMINA ss1958505651 Feb 12, 2016 (147)
24 HUMAN_LONGEVITY ss2239249283 Dec 20, 2016 (150)
25 ILLUMINA ss2633741232 Nov 08, 2017 (151)
26 GNOMAD ss2746877086 Nov 08, 2017 (151)
27 GNOMAD ss2786463119 Nov 08, 2017 (151)
28 AFFY ss2985199856 Nov 08, 2017 (151)
29 ILLUMINA ss3022070213 Nov 08, 2017 (151)
30 ILLUMINA ss3628288911 Oct 11, 2018 (152)
31 ILLUMINA ss3631701173 Oct 11, 2018 (152)
32 ILLUMINA ss3634812421 Oct 11, 2018 (152)
33 ILLUMINA ss3640519720 Oct 11, 2018 (152)
34 ILLUMINA ss3644769119 Oct 11, 2018 (152)
35 ILLUMINA ss3652521294 Oct 11, 2018 (152)
36 ILLUMINA ss3653967589 Oct 11, 2018 (152)
37 EVA_DECODE ss3706045812 Jul 13, 2019 (153)
38 ILLUMINA ss3725873182 Jul 13, 2019 (153)
39 ILLUMINA ss3744487005 Jul 13, 2019 (153)
40 ILLUMINA ss3745112248 Jul 13, 2019 (153)
41 PAGE_CC ss3770986623 Jul 13, 2019 (153)
42 ILLUMINA ss3772608750 Jul 13, 2019 (153)
43 KHV_HUMAN_GENOMES ss3802462329 Jul 13, 2019 (153)
44 EVA ss3823853947 Apr 25, 2020 (154)
45 SGDP_PRJ ss3854619233 Apr 25, 2020 (154)
46 EVA ss3986214626 Apr 26, 2021 (155)
47 TOPMED ss4545058632 Apr 26, 2021 (155)
48 1000G_HIGH_COVERAGE ss5252074559 Oct 12, 2022 (156)
49 TRAN_CS_UWATERLOO ss5314404709 Oct 12, 2022 (156)
50 EVA ss5336113370 Oct 12, 2022 (156)
51 HUGCELL_USP ss5451681215 Oct 12, 2022 (156)
52 1000G_HIGH_COVERAGE ss5529443819 Oct 12, 2022 (156)
53 SANFORD_IMAGENETICS ss5630976859 Oct 12, 2022 (156)
54 EVA ss5847903015 Oct 12, 2022 (156)
55 EVA ss5934755183 Oct 12, 2022 (156)
56 EVA ss5957233586 Oct 12, 2022 (156)
57 1000Genomes NC_000002.11 - 219204854 Oct 11, 2018 (152)
58 1000Genomes_30x NC_000002.12 - 218340131 Oct 12, 2022 (156)
59 ExAC NC_000002.11 - 219204854 Oct 11, 2018 (152)
60 gnomAD - Genomes NC_000002.12 - 218340131 Apr 26, 2021 (155)
61 gnomAD - Exomes NC_000002.11 - 219204854 Jul 13, 2019 (153)
62 GO Exome Sequencing Project NC_000002.11 - 219204854 Oct 11, 2018 (152)
63 The PAGE Study NC_000002.12 - 218340131 Jul 13, 2019 (153)
64 Qatari NC_000002.11 - 219204854 Apr 25, 2020 (154)
65 SGDP_PRJ NC_000002.11 - 219204854 Apr 25, 2020 (154)
66 TopMed NC_000002.12 - 218340131 Apr 26, 2021 (155)
67 ALFA NC_000002.12 - 218340131 Apr 26, 2021 (155)
68 ClinVar RCV000272595.8 Oct 12, 2022 (156)
69 ClinVar RCV000857916.6 Oct 12, 2022 (156)
70 ClinVar RCV001598655.3 Oct 12, 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
ss118082290, ss201754564, ss484015482 NC_000002.10:218913097:G:A NC_000002.12:218340130:G:A (self)
12799829, 6632846, 2388705, 312359, 3259948, 6636213, ss219819760, ss342098321, ss480591584, ss489851640, ss491331150, ss533831645, ss556227671, ss779085178, ss780810239, ss781269194, ss783492048, ss834548970, ss1301692879, ss1686728666, ss1752339094, ss1917759716, ss1921218018, ss1946066455, ss1958505651, ss2633741232, ss2746877086, ss2786463119, ss2985199856, ss3022070213, ss3628288911, ss3631701173, ss3634812421, ss3640519720, ss3644769119, ss3652521294, ss3653967589, ss3744487005, ss3745112248, ss3772608750, ss3823853947, ss3854619233, ss3986214626, ss5336113370, ss5630976859, ss5847903015, ss5957233586 NC_000002.11:219204853:G:A NC_000002.12:218340130:G:A (self)
RCV000272595.8, RCV000857916.6, RCV001598655.3, 16969754, 91267487, 208092, 348881511, 12995755182, ss2239249283, ss3706045812, ss3725873182, ss3770986623, ss3802462329, ss4545058632, ss5252074559, ss5314404709, ss5451681215, ss5529443819, ss5934755183 NC_000002.12:218340130:G:A NC_000002.12:218340130:G:A (self)
ss159703675 NT_005403.17:69414271:G:A NC_000002.12:218340130:G:A (self)
12995755182 NC_000002.12:218340130:G:C NC_000002.12:218340130:G:C (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 rs73990423

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