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dbSNP Short Genetic Variations

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.


Current Build 153

Released July 9, 2019

Homo sapiens
chr3:120670582 (GRCh38.p12) 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.

Variation Type
SNV Single Nucleotide Variation
A=0.03171 (7900/249102, GnomAD_exome)
A=0.02337 (2934/125568, TOPMED)
A=0.03134 (3765/120124, ExAC) (+ 7 more)
A=0.0296 (928/31398, GnomAD)
A=0.0255 (331/12998, GO-ESP)
A=0.019 (96/5008, 1000G)
A=0.043 (192/4480, Estonian)
A=0.032 (123/3854, ALSPAC)
A=0.033 (124/3708, TWINSUK)
A=0.03 (18/600, NorthernSweden)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
HGD : Intron Variant
0 citations
Genomic View
See rs on genome

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.p12 chr 3 NC_000003.12:g.120670582G>A
GRCh37.p13 chr 3 NC_000003.11:g.120389429G>A
HGD RefSeqGene NG_011957.1:g.16900C>T
Gene: HGD, homogentisate 1,2-dioxygenase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
HGD transcript NM_000187.4:c. N/A Intron Variant
HGD transcript variant X1 XM_005247412.2:c. N/A Intron Variant
HGD transcript variant X2 XM_005247413.2:c. N/A Intron Variant
HGD transcript variant X5 XM_005247414.5:c. N/A Intron Variant
HGD transcript variant X4 XM_011512746.2:c. N/A Intron Variant
HGD transcript variant X3 XM_017006277.2:c. N/A Intron Variant

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

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").

Study Population Group Sample Size Ref Allele Alt Allele
gnomAD - Exomes Global Study-wide 249102 G=0.96829 A=0.03171
gnomAD - Exomes European Sub 133662 G=0.96168 A=0.03832
gnomAD - Exomes Asian Sub 48794 G=0.9752 A=0.0248
gnomAD - Exomes American Sub 34352 G=0.9822 A=0.0178
gnomAD - Exomes African Sub 16186 G=0.9912 A=0.0088
gnomAD - Exomes Ashkenazi Jewish Sub 10038 G=0.9451 A=0.0549
gnomAD - Exomes Other Sub 6070 G=0.956 A=0.044
TopMed Global Study-wide 125568 G=0.97663 A=0.02337
ExAC Global Study-wide 120124 G=0.96866 A=0.03134
ExAC Europe Sub 72646 G=0.9618 A=0.0382
ExAC Asian Sub 24898 G=0.9739 A=0.0261
ExAC American Sub 11344 G=0.9833 A=0.0167
ExAC African Sub 10336 G=0.9911 A=0.0089
ExAC Other Sub 900 G=0.93 A=0.07
gnomAD - Genomes Global Study-wide 31398 G=0.9704 A=0.0296
gnomAD - Genomes European Sub 18900 G=0.9586 A=0.0414
gnomAD - Genomes African Sub 8714 G=0.993 A=0.007
gnomAD - Genomes East Asian Sub 1560 G=0.999 A=0.001
gnomAD - Genomes Other Sub 1088 G=0.967 A=0.033
gnomAD - Genomes American Sub 848 G=0.98 A=0.02
gnomAD - Genomes Ashkenazi Jewish Sub 288 G=0.92 A=0.08
GO Exome Sequencing Project Global Study-wide 12998 G=0.9745 A=0.0255
GO Exome Sequencing Project European American Sub 8592 G=0.966 A=0.034
GO Exome Sequencing Project African American Sub 4406 G=0.992 A=0.008
1000Genomes Global Study-wide 5008 G=0.981 A=0.019
1000Genomes African Sub 1322 G=0.994 A=0.006
1000Genomes East Asian Sub 1008 G=1.000 A=0.000
1000Genomes Europe Sub 1006 G=0.963 A=0.037
1000Genomes South Asian Sub 978 G=0.97 A=0.03
1000Genomes American Sub 694 G=0.97 A=0.03
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.957 A=0.043
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.968 A=0.032
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.967 A=0.033
Northern Sweden ACPOP Study-wide 600 G=0.97 A=0.03

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 Note
GRCh38.p12 chr 3 NC_000003.12:g.120670582= NC_000003.12:g.12067058...


GRCh37.p13 chr 3 NC_000003.11:g.120389429= NC_000003.11:g.12038942...


HGD RefSeqGene NG_011957.1:g.16900= NG_011957.1:g.16900C>T

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#.

31 SubSNP, 10 Frequency submissions
No Submitter Submission ID Date (Build)
1 GMI ss284734959 Apr 25, 2013 (138)
2 1000GENOMES ss331004978 May 09, 2011 (134)
3 1000GENOMES ss489894728 May 04, 2012 (137)
4 ILLUMINA ss536439061 Sep 08, 2015 (146)
5 NHLBI-ESP ss712547081 Apr 25, 2013 (138)
6 EVA-GONL ss979083942 Aug 21, 2014 (142)
7 JMKIDD_LAB ss1070777393 Aug 21, 2014 (142)
8 1000GENOMES ss1305860188 Aug 21, 2014 (142)
9 EVA_GENOME_DK ss1580152580 Apr 01, 2015 (144)
10 EVA_DECODE ss1588566161 Apr 01, 2015 (144)
11 EVA_UK10K_ALSPAC ss1608059712 Apr 01, 2015 (144)
12 EVA_UK10K_TWINSUK ss1651053745 Apr 01, 2015 (144)
13 EVA_EXAC ss1687158547 Apr 01, 2015 (144)
14 EVA_MGP ss1711029907 Apr 01, 2015 (144)
15 WEILL_CORNELL_DGM ss1922310272 Feb 12, 2016 (147)
16 JJLAB ss2021722973 Sep 14, 2016 (149)
17 USC_VALOUEV ss2149815108 Dec 20, 2016 (150)
18 HUMAN_LONGEVITY ss2255254808 Dec 20, 2016 (150)
19 TOPMED ss2422579240 Dec 20, 2016 (150)
20 GNOMAD ss2733990667 Nov 08, 2017 (151)
21 GNOMAD ss2747077650 Nov 08, 2017 (151)
22 GNOMAD ss2798281808 Nov 08, 2017 (151)
23 SWEGEN ss2993074628 Nov 08, 2017 (151)
24 CSHL ss3345231491 Nov 08, 2017 (151)
25 TOPMED ss3403602885 Nov 08, 2017 (151)
26 ILLUMINA ss3628759194 Oct 12, 2018 (152)
27 OMUKHERJEE_ADBS ss3646291551 Oct 12, 2018 (152)
28 EGCUT_WGS ss3661001394 Jul 13, 2019 (153)
29 EVA_DECODE ss3710145731 Jul 13, 2019 (153)
30 ACPOP ss3730286857 Jul 13, 2019 (153)
31 KHV_HUMAN_GENOMES ss3803735811 Jul 13, 2019 (153)
32 1000Genomes NC_000003.11 - 120389429 Oct 12, 2018 (152)
33 The Avon Longitudinal Study of Parents and Children NC_000003.11 - 120389429 Oct 12, 2018 (152)
34 Genetic variation in the Estonian population NC_000003.11 - 120389429 Oct 12, 2018 (152)
35 ExAC NC_000003.11 - 120389429 Oct 12, 2018 (152)
36 gnomAD - Genomes NC_000003.11 - 120389429 Jul 13, 2019 (153)
37 gnomAD - Exomes NC_000003.11 - 120389429 Jul 13, 2019 (153)
38 GO Exome Sequencing Project NC_000003.11 - 120389429 Oct 12, 2018 (152)
39 Northern Sweden NC_000003.11 - 120389429 Jul 13, 2019 (153)
40 TopMed NC_000003.12 - 120670582 Oct 12, 2018 (152)
41 UK 10K study - Twins NC_000003.11 - 120389429 Oct 12, 2018 (152)

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
ss284734959, ss1588566161 NC_000003.10:121872118:G:A NC_000003.12:120670581:G:A (self)
17112883, 9532636, 6739642, 7094479, 46817358, 3076166, 403778, 3571722, 9532636, ss331004978, ss489894728, ss536439061, ss712547081, ss979083942, ss1070777393, ss1305860188, ss1580152580, ss1608059712, ss1651053745, ss1687158547, ss1711029907, ss1922310272, ss2021722973, ss2149815108, ss2422579240, ss2733990667, ss2747077650, ss2798281808, ss2993074628, ss3345231491, ss3628759194, ss3646291551, ss3661001394, ss3730286857 NC_000003.11:120389428:G:A NC_000003.12:120670581:G:A (self)
261524259, ss2255254808, ss3403602885, ss3710145731, ss3803735811 NC_000003.12:120670581:G:A NC_000003.12:120670581:G:A (self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs145728491

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.post246+3cda961