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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.

rs376858353

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr3:120670584 (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
G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.00028 (70/249108, GnomAD_exome)
T=0.00105 (132/125568, TOPMED)
T=0.00029 (35/120148, ExAC) (+ 4 more)
T=0.0010 (31/31394, GnomAD)
T=0.001 (8/7264, GO-ESP)
T=0.001 (3/5008, 1000G)
T=0.000 (1/4480, Estonian)
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.120670584G>T
GRCh37.p13 chr 3 NC_000003.11:g.120389431G>T
HGD RefSeqGene NG_011957.1:g.16898C>A
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
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

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 249108 G=0.99972 T=0.00028
gnomAD - Exomes European Sub 133684 G=0.99997 T=0.00003
gnomAD - Exomes Asian Sub 48794 G=0.9999 T=0.0001
gnomAD - Exomes American Sub 34354 G=0.9998 T=0.0002
gnomAD - Exomes African Sub 16170 G=0.9967 T=0.0033
gnomAD - Exomes Ashkenazi Jewish Sub 10038 G=1.0000 T=0.0000
gnomAD - Exomes Other Sub 6068 G=1.000 T=0.000
TopMed Global Study-wide 125568 G=0.99895 T=0.00105
ExAC Global Study-wide 120148 G=0.99971 T=0.00029
ExAC Europe Sub 72678 G=1.0000 T=0.0000
ExAC Asian Sub 24900 G=1.0000 T=0.0000
ExAC American Sub 11344 G=0.9998 T=0.0002
ExAC African Sub 10324 G=0.9970 T=0.0030
ExAC Other Sub 902 G=1.00 T=0.00
gnomAD - Genomes Global Study-wide 31394 G=0.9990 T=0.0010
gnomAD - Genomes European Sub 18900 G=0.9998 T=0.0002
gnomAD - Genomes African Sub 8708 G=0.997 T=0.003
gnomAD - Genomes East Asian Sub 1560 G=1.000 T=0.000
gnomAD - Genomes Other Sub 1088 G=1.000 T=0.000
gnomAD - Genomes American Sub 848 G=1.00 T=0.00
gnomAD - Genomes Ashkenazi Jewish Sub 290 G=1.00 T=0.00
GO Exome Sequencing Project Global Study-wide 7264 G=0.999 T=0.001
GO Exome Sequencing Project European American Sub 4610 G=1.000 T=0.000
GO Exome Sequencing Project African American Sub 2654 G=0.997 T=0.003
1000Genomes Global Study-wide 5008 G=0.999 T=0.001
1000Genomes African Sub 1322 G=0.998 T=0.002
1000Genomes East Asian Sub 1008 G=1.000 T=0.000
1000Genomes Europe Sub 1006 G=1.000 T=0.000
1000Genomes South Asian Sub 978 G=1.00 T=0.00
1000Genomes American Sub 694 G=1.00 T=0.00
Genetic variation in the Estonian population Estonian Study-wide 4480 G=1.000 T=0.000
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= T Note
GRCh38.p12 chr 3 NC_000003.12:g.120670584= NC_000003.12:g.12067058...

NC_000003.12:g.120670584G>T

GRCh37.p13 chr 3 NC_000003.11:g.120389431= NC_000003.11:g.12038943...

NC_000003.11:g.120389431G>T

HGD RefSeqGene NG_011957.1:g.16898= NG_011957.1:g.16898C>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#.

11 SubSNP, 7 Frequency submissions
No Submitter Submission ID Date (Build)
1 NHLBI-ESP ss712540865 Apr 25, 2013 (138)
2 1000GENOMES ss1305860189 Aug 21, 2014 (142)
3 EVA_EXAC ss1687158548 Apr 01, 2015 (144)
4 WEILL_CORNELL_DGM ss1922310273 Feb 12, 2016 (147)
5 HUMAN_LONGEVITY ss2255254809 Dec 20, 2016 (150)
6 TOPMED ss2422579241 Dec 20, 2016 (150)
7 GNOMAD ss2733990668 Nov 08, 2017 (151)
8 GNOMAD ss2747077651 Nov 08, 2017 (151)
9 GNOMAD ss2798281809 Nov 08, 2017 (151)
10 TOPMED ss3403602887 Nov 08, 2017 (151)
11 EGCUT_WGS ss3661001395 Jul 13, 2019 (153)
12 1000Genomes NC_000003.11 - 120389431 Oct 12, 2018 (152)
13 Genetic variation in the Estonian population NC_000003.11 - 120389431 Oct 12, 2018 (152)
14 ExAC NC_000003.11 - 120389431 Oct 12, 2018 (152)
15 gnomAD - Genomes NC_000003.11 - 120389431 Jul 13, 2019 (153)
16 gnomAD - Exomes NC_000003.11 - 120389431 Jul 13, 2019 (153)
17 GO Exome Sequencing Project NC_000003.11 - 120389431 Oct 12, 2018 (152)
18 TopMed NC_000003.12 - 120670584 Oct 12, 2018 (152)
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
17112884, 6739643, 7094480, 46817359, 3076167, 403779, ss712540865, ss1305860189, ss1687158548, ss1922310273, ss2422579241, ss2733990668, ss2747077651, ss2798281809, ss3661001395 NC_000003.11:120389430:G:T NC_000003.12:120670583:G:T (self)
261524261, ss2255254809, ss3403602887 NC_000003.12:120670583:G:T NC_000003.12:120670583:G: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 rs376858353

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