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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.

rs376223608

Current Build 154

Released April 21, 2020

Organism
Homo sapiens
Position
chr3:120646236 (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.

Alleles
C>A / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.001952 (490/251008, GnomAD_exome)
T=0.002071 (260/125568, TOPMED)
T=0.001786 (216/120974, ExAC) (+ 8 more)
T=0.00166 (52/31404, GnomAD)
T=0.00223 (29/13006, GO-ESP)
T=0.00519 (58/11176, ALFA Project)
T=0.0009 (4/4480, Estonian)
T=0.0042 (16/3854, ALSPAC)
T=0.0024 (9/3708, TWINSUK)
T=0.003 (3/998, GoNL)
T=0.002 (1/534, MGP)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
HGD : Intron Variant
Publications
0 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.p12 chr 3 NC_000003.12:g.120646236C>A
GRCh38.p12 chr 3 NC_000003.12:g.120646236C>T
GRCh37.p13 chr 3 NC_000003.11:g.120365083C>A
GRCh37.p13 chr 3 NC_000003.11:g.120365083C>T
HGD RefSeqGene NG_011957.1:g.41246G>T
HGD RefSeqGene NG_011957.1:g.41246G>A
Gene: HGD, homogentisate 1,2-dioxygenase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
HGD transcript NM_000187.4:c.649+31G>T N/A Intron Variant
HGD transcript variant X1 XM_005247412.2:c.549+737G…

XM_005247412.2:c.549+737G>T

N/A Intron Variant
HGD transcript variant X2 XM_005247413.2:c.649+31G>T N/A Intron Variant
HGD transcript variant X5 XM_005247414.5:c.649+31G>T N/A Intron Variant
HGD transcript variant X4 XM_011512746.2:c.649+31G>T N/A Intron Variant
HGD transcript variant X3 XM_017006277.2:c.226+31G>T 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 (New)
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 28178 C=0.99620 T=0.00380
European Sub 20348 C=0.99582 T=0.00418
African Sub 3564 C=0.9989 T=0.0011
African Others Sub 122 C=1.000 T=0.000
African American Sub 3442 C=0.9988 T=0.0012
Asian Sub 172 C=1.000 T=0.000
East Asian Sub 114 C=1.000 T=0.000
Other Asian Sub 58 C=1.00 T=0.00
Latin American 1 Sub 154 C=0.994 T=0.006
Latin American 2 Sub 616 C=1.000 T=0.000
South Asian Sub 98 C=1.00 T=0.00
Other Sub 3226 C=0.9947 T=0.0053


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
gnomAD - Exomes Global Study-wide 251008 C=0.998048 T=0.001952
gnomAD - Exomes European Sub 135020 C=0.997786 T=0.002214
gnomAD - Exomes Asian Sub 48964 C=0.99994 T=0.00006
gnomAD - Exomes American Sub 34576 C=0.99910 T=0.00090
gnomAD - Exomes African Sub 16252 C=0.99908 T=0.00092
gnomAD - Exomes Ashkenazi Jewish Sub 10072 C=0.98719 T=0.01281
gnomAD - Exomes Other Sub 6124 C=0.9979 T=0.0021
TopMed Global Study-wide 125568 C=0.997929 T=0.002071
ExAC Global Study-wide 120974 C=0.998214 T=0.001786
ExAC Europe Sub 73162 C=0.99739 T=0.00261
ExAC Asian Sub 25004 C=0.99996 T=0.00004
ExAC American Sub 11528 C=0.99931 T=0.00069
ExAC African Sub 10380 C=0.99884 T=0.00116
ExAC Other Sub 900 C=0.996 T=0.004
gnomAD - Genomes Global Study-wide 31404 C=0.99834 T=0.00166
gnomAD - Genomes European Sub 18910 C=0.99799 T=0.00201
gnomAD - Genomes African Sub 8710 C=0.9997 T=0.0003
gnomAD - Genomes East Asian Sub 1560 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 1088 C=0.9963 T=0.0037
gnomAD - Genomes American Sub 846 C=0.999 T=0.001
gnomAD - Genomes Ashkenazi Jewish Sub 290 C=0.979 T=0.021
GO Exome Sequencing Project Global Study-wide 13006 C=0.99777 T=0.00223
GO Exome Sequencing Project European American Sub 8600 C=0.9972 T=0.0028
GO Exome Sequencing Project African American Sub 4406 C=0.9989 T=0.0011
ALFA Total Global 11176 C=0.99481 T=0.00519
ALFA European Sub 8134 C=0.9948 T=0.0052
ALFA Other Sub 2302 C=0.9939 T=0.0061
ALFA African Sub 676 C=0.997 T=0.003
ALFA Asian Sub 60 C=1.00 T=0.00
ALFA South Asian Sub 4 C=1.0 T=0.0
ALFA Latin American 1 Sub 0 C=0 T=0
ALFA Latin American 2 Sub 0 C=0 T=0
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.9991 T=0.0009
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9958 T=0.0042
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.9976 T=0.0024
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.997 T=0.003
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 C=0.998 T=0.002
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 C= A T
GRCh38.p12 chr 3 NC_000003.12:g.120646236= NC_000003.12:g.120646236C>A NC_000003.12:g.120646236C>T
GRCh37.p13 chr 3 NC_000003.11:g.120365083= NC_000003.11:g.120365083C>A NC_000003.11:g.120365083C>T
HGD RefSeqGene NG_011957.1:g.41246= NG_011957.1:g.41246G>T NG_011957.1:g.41246G>A
HGD transcript NM_000187.3:c.649+31= NM_000187.3:c.649+31G>T NM_000187.3:c.649+31G>A
HGD transcript NM_000187.4:c.649+31= NM_000187.4:c.649+31G>T NM_000187.4:c.649+31G>A
HGD transcript variant X1 XM_005247412.1:c.549+737= XM_005247412.1:c.549+737G>T XM_005247412.1:c.549+737G>A
HGD transcript variant X1 XM_005247412.2:c.549+737= XM_005247412.2:c.549+737G>T XM_005247412.2:c.549+737G>A
HGD transcript variant X2 XM_005247413.1:c.649+31= XM_005247413.1:c.649+31G>T XM_005247413.1:c.649+31G>A
HGD transcript variant X2 XM_005247413.2:c.649+31= XM_005247413.2:c.649+31G>T XM_005247413.2:c.649+31G>A
HGD transcript variant X3 XM_005247414.1:c.649+31= XM_005247414.1:c.649+31G>T XM_005247414.1:c.649+31G>A
HGD transcript variant X5 XM_005247414.5:c.649+31= XM_005247414.5:c.649+31G>T XM_005247414.5:c.649+31G>A
HGD transcript variant X4 XM_011512746.2:c.649+31= XM_011512746.2:c.649+31G>T XM_011512746.2:c.649+31G>A
HGD transcript variant X3 XM_017006277.2:c.226+31= XM_017006277.2:c.226+31G>T XM_017006277.2:c.226+31G>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#.

20 SubSNP, 11 Frequency submissions
No Submitter Submission ID Date (Build)
1 ILLUMINA ss535048638 Sep 08, 2015 (146)
2 NHLBI-ESP ss712547032 Apr 25, 2013 (138)
3 EVA-GONL ss979083745 Aug 21, 2014 (142)
4 EVA_DECODE ss1588565956 Apr 01, 2015 (144)
5 EVA_UK10K_ALSPAC ss1608059320 Apr 01, 2015 (144)
6 EVA_UK10K_TWINSUK ss1651053353 Apr 01, 2015 (144)
7 EVA_EXAC ss1687158363 Apr 01, 2015 (144)
8 EVA_MGP ss1711029891 Apr 01, 2015 (144)
9 JJLAB ss2021722839 Sep 14, 2016 (149)
10 HUMAN_LONGEVITY ss2255253377 Dec 20, 2016 (150)
11 TOPMED ss2422577790 Dec 20, 2016 (150)
12 GNOMAD ss2733990413 Nov 08, 2017 (151)
13 GNOMAD ss2747077571 Nov 08, 2017 (151)
14 GNOMAD ss2798280005 Nov 08, 2017 (151)
15 SWEGEN ss2993074361 Nov 08, 2017 (151)
16 TOPMED ss3403598592 Nov 08, 2017 (151)
17 ILLUMINA ss3628759146 Oct 12, 2018 (152)
18 EGCUT_WGS ss3661001072 Jul 13, 2019 (153)
19 EVA_DECODE ss3710145404 Jul 13, 2019 (153)
20 EVA ss3823945419 Apr 25, 2020 (154)
21 The Avon Longitudinal Study of Parents and Children NC_000003.11 - 120365083 Oct 12, 2018 (152)
22 Genetic variation in the Estonian population NC_000003.11 - 120365083 Oct 12, 2018 (152)
23 ExAC NC_000003.11 - 120365083 Oct 12, 2018 (152)
24 gnomAD - Genomes NC_000003.11 - 120365083 Jul 13, 2019 (153)
25 gnomAD - Exomes NC_000003.11 - 120365083 Jul 13, 2019 (153)
26 GO Exome Sequencing Project NC_000003.11 - 120365083 Oct 12, 2018 (152)
27 Genome of the Netherlands Release 5 NC_000003.11 - 120365083 Apr 25, 2020 (154)
28 Medical Genome Project healthy controls from Spanish population NC_000003.11 - 120365083 Apr 25, 2020 (154)
29 TopMed NC_000003.12 - 120646236 Oct 12, 2018 (152)
30 UK 10K study - Twins NC_000003.11 - 120365083 Oct 12, 2018 (152)
31 dbGaP Population Frequency Project NC_000003.12 - 120646236 Apr 25, 2020 (154)
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
ss2733990413 NC_000003.11:120365082:C:A NC_000003.12:120646235:C:A (self)
ss1588565956 NC_000003.10:121847772:C:T NC_000003.12:120646235:C:T (self)
9532208, 6739320, 7094287, 46815526, 3075891, 403725, 4187772, 145722, 9532208, ss535048638, ss712547032, ss979083745, ss1608059320, ss1651053353, ss1687158363, ss1711029891, ss2021722839, ss2422577790, ss2733990413, ss2747077571, ss2798280005, ss2993074361, ss3628759146, ss3661001072, ss3823945419 NC_000003.11:120365082:C:T NC_000003.12:120646235:C:T (self)
261520644, 16124177, ss2255253377, ss3403598592, ss3710145404 NC_000003.12:120646235:C:T NC_000003.12:120646235:C: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 rs376223608

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.post557+f76c771