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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 Aliases 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.


Current Build 153

Released July 9, 2019

Homo sapiens
chr3:149837794 (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
T=0.02639 (3314/125568, TOPMED)
T=0.0235 (736/31350, GnomAD)
T=0.026 (130/5008, 1000G) (+ 2 more)
T=0.000 (1/3854, ALSPAC)
T=0.001 (2/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
RNF13 : 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.149837794C>T
GRCh37.p13 chr 3 NC_000003.11:g.149555581C>T
Gene: RNF13, ring finger protein 13 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
RNF13 transcript variant 1 NM_007282.4:c. N/A Intron Variant
RNF13 transcript variant 4 NM_183381.2:c. N/A Intron Variant
RNF13 transcript variant 3 NM_183383.2:c. N/A Intron Variant
RNF13 transcript variant X6 XM_005247092.4:c. N/A Intron Variant
RNF13 transcript variant X1 XM_011512373.2:c. N/A Intron Variant
RNF13 transcript variant X4 XM_011512374.2:c. N/A Intron Variant
RNF13 transcript variant X9 XM_011512376.2:c. N/A Intron Variant
RNF13 transcript variant X2 XM_017005654.1:c. N/A Intron Variant
RNF13 transcript variant X3 XM_017005655.1:c. N/A Intron Variant
RNF13 transcript variant X7 XM_017005656.1:c. N/A Intron Variant
RNF13 transcript variant X8 XM_017005657.1:c. N/A Intron Variant
RNF13 transcript variant X10 XM_017005658.1:c. N/A Intron Variant
RNF13 transcript variant X12 XM_017005660.1:c. N/A Intron Variant
RNF13 transcript variant X5 XM_024453332.1:c. N/A Intron Variant
RNF13 transcript variant X15 XM_017005661.2:c. N/A Genic Upstream Transcript Variant
RNF13 transcript variant X13 XR_001739990.2:n. N/A Intron Variant
RNF13 transcript variant X14 XR_002959487.1:n. 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
TopMed Global Study-wide 125568 C=0.97361 T=0.02639
gnomAD - Genomes Global Study-wide 31350 C=0.9765 T=0.0235
gnomAD - Genomes European Sub 18900 C=0.9998 T=0.0002
gnomAD - Genomes African Sub 8672 C=0.917 T=0.083
gnomAD - Genomes East Asian Sub 1554 C=1.000 T=0.000
gnomAD - Genomes Other Sub 1086 C=0.994 T=0.006
gnomAD - Genomes American Sub 848 C=0.99 T=0.01
gnomAD - Genomes Ashkenazi Jewish Sub 290 C=1.00 T=0.00
1000Genomes Global Study-wide 5008 C=0.974 T=0.026
1000Genomes African Sub 1322 C=0.906 T=0.094
1000Genomes East Asian Sub 1008 C=1.000 T=0.000
1000Genomes Europe Sub 1006 C=1.000 T=0.000
1000Genomes South Asian Sub 978 C=1.00 T=0.00
1000Genomes American Sub 694 C=0.99 T=0.01
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=1.000 T=0.000
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.999 T=0.001

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= T Note
GRCh38.p12 chr 3 NC_000003.12:g.149837794= NC_000003.12:g.14983779...


GRCh37.p13 chr 3 NC_000003.11:g.149555581= NC_000003.11:g.14955558...



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#.

12 SubSNP, 5 Frequency submissions
No Submitter Submission ID Date (Build)
1 COMPLETE_GENOMICS ss164595448 Jul 04, 2010 (132)
2 1000GENOMES ss331142832 May 09, 2011 (142)
3 JMKIDD_LAB ss1070933812 Aug 21, 2014 (142)
4 1000GENOMES ss1306677692 Aug 21, 2014 (142)
5 EVA_UK10K_ALSPAC ss1608487866 Apr 01, 2015 (144)
6 EVA_UK10K_TWINSUK ss1651481899 Apr 01, 2015 (144)
7 WEILL_CORNELL_DGM ss1922519775 Feb 12, 2016 (147)
8 HUMAN_LONGEVITY ss2256909435 Dec 20, 2016 (150)
9 TOPMED ss2424289545 Dec 20, 2016 (150)
10 GNOMAD ss2800612202 Nov 08, 2017 (151)
11 TOPMED ss3408930392 Nov 08, 2017 (151)
12 KHV_HUMAN_GENOMES ss3803986386 Jul 13, 2019 (153)
13 1000Genomes NC_000003.11 - 149555581 Oct 12, 2018 (152)
14 The Avon Longitudinal Study of Parents and Children NC_000003.11 - 149555581 Oct 12, 2018 (152)
15 gnomAD - Genomes NC_000003.11 - 149555581 Jul 13, 2019 (153)
16 TopMed NC_000003.12 - 149837794 Oct 12, 2018 (152)
17 UK 10K study - Twins NC_000003.11 - 149555581 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).

Associated ID History Updated (Build)
rs138389984 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss164595448 NC_000003.10:151038270:C:T NC_000003.12:149837793:C:T (self)
17959811, 10003052, 49129689, 10003052, ss331142832, ss1070933812, ss1306677692, ss1608487866, ss1651481899, ss1922519775, ss2424289545, ss2800612202 NC_000003.11:149555580:C:T NC_000003.12:149837793:C:T (self)
265947983, ss2256909435, ss3408930392, ss3803986386 NC_000003.12:149837793:C:T NC_000003.12:149837793:C:T (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 rs112797680

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.post308+0fe9b3b