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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.

rs117250923

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr3:149892399 (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
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.003332 (882/264690, TOPMED)
A=0.002261 (317/140222, GnomAD)
A=0.07708 (2178/28258, 14KJPN) (+ 8 more)
A=0.07434 (1246/16760, 8.3KJPN)
A=0.00125 (18/14420, ALFA)
A=0.0176 (113/6404, 1000G_30x)
A=0.0202 (101/5008, 1000G)
A=0.0679 (199/2930, KOREAN)
A=0.134 (29/216, Vietnamese)
G=0.50 (9/18, SGDP_PRJ)
A=0.50 (9/18, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
RNF13 : Intron 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 14420 G=0.99875 A=0.00125
European Sub 9824 G=0.9999 A=0.0001
African Sub 2946 G=1.0000 A=0.0000
African Others Sub 114 G=1.000 A=0.000
African American Sub 2832 G=1.0000 A=0.0000
Asian Sub 112 G=0.911 A=0.089
East Asian Sub 86 G=0.88 A=0.12
Other Asian Sub 26 G=1.00 A=0.00
Latin American 1 Sub 146 G=1.000 A=0.000
Latin American 2 Sub 610 G=1.000 A=0.000
South Asian Sub 98 G=1.00 A=0.00
Other Sub 684 G=0.990 A=0.010


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=0.996668 A=0.003332
gnomAD - Genomes Global Study-wide 140222 G=0.997739 A=0.002261
gnomAD - Genomes European Sub 75940 G=1.00000 A=0.00000
gnomAD - Genomes African Sub 42024 G=0.99993 A=0.00007
gnomAD - Genomes American Sub 13652 G=0.99978 A=0.00022
gnomAD - Genomes Ashkenazi Jewish Sub 3320 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3134 G=0.9033 A=0.0967
gnomAD - Genomes Other Sub 2152 G=0.9963 A=0.0037
14KJPN JAPANESE Study-wide 28258 G=0.92292 A=0.07708
8.3KJPN JAPANESE Study-wide 16760 G=0.92566 A=0.07434
Allele Frequency Aggregator Total Global 14420 G=0.99875 A=0.00125
Allele Frequency Aggregator European Sub 9824 G=0.9999 A=0.0001
Allele Frequency Aggregator African Sub 2946 G=1.0000 A=0.0000
Allele Frequency Aggregator Other Sub 684 G=0.990 A=0.010
Allele Frequency Aggregator Latin American 2 Sub 610 G=1.000 A=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 G=1.000 A=0.000
Allele Frequency Aggregator Asian Sub 112 G=0.911 A=0.089
Allele Frequency Aggregator South Asian Sub 98 G=1.00 A=0.00
1000Genomes_30x Global Study-wide 6404 G=0.9824 A=0.0176
1000Genomes_30x African Sub 1786 G=0.9989 A=0.0011
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=0.9051 A=0.0949
1000Genomes_30x American Sub 980 G=1.000 A=0.000
1000Genomes Global Study-wide 5008 G=0.9798 A=0.0202
1000Genomes African Sub 1322 G=0.9985 A=0.0015
1000Genomes East Asian Sub 1008 G=0.9018 A=0.0982
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=1.000 A=0.000
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.9321 A=0.0679
A Vietnamese Genetic Variation Database Global Study-wide 216 G=0.866 A=0.134
SGDP_PRJ Global Study-wide 18 G=0.50 A=0.50
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 3 NC_000003.12:g.149892399G>A
GRCh37.p13 chr 3 NC_000003.11:g.149610186G>A
Gene: RNF13, ring finger protein 13 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
RNF13 transcript variant 5 NM_001378285.1:c.322-3074…

NM_001378285.1:c.322-3074G>A

N/A Intron Variant
RNF13 transcript variant 6 NM_001378286.1:c.322-3074…

NM_001378286.1:c.322-3074G>A

N/A Intron Variant
RNF13 transcript variant 7 NM_001378287.1:c.-46-3074…

NM_001378287.1:c.-46-3074G>A

N/A Intron Variant
RNF13 transcript variant 8 NM_001378288.1:c.-46-3074…

NM_001378288.1:c.-46-3074G>A

N/A Intron Variant
RNF13 transcript variant 9 NM_001378289.1:c.-46-3074…

NM_001378289.1:c.-46-3074G>A

N/A Intron Variant
RNF13 transcript variant 10 NM_001378290.1:c.-46-3074…

NM_001378290.1:c.-46-3074G>A

N/A Intron Variant
RNF13 transcript variant 11 NM_001378291.1:c.-72-3074…

NM_001378291.1:c.-72-3074G>A

N/A Intron Variant
RNF13 transcript variant 1 NM_007282.4:c.322-3074G>A N/A Intron Variant
RNF13 transcript variant 4 NM_183381.3:c.322-3074G>A N/A Intron Variant
RNF13 transcript variant 3 NM_183383.2:c.-46-3074G>A N/A Intron Variant
RNF13 transcript variant 12 NR_165474.1:n. N/A Intron Variant
RNF13 transcript variant X3 XM_011512373.3:c.322-3074…

XM_011512373.3:c.322-3074G>A

N/A Intron Variant
RNF13 transcript variant X1 XM_047447379.1:c.322-3074…

XM_047447379.1:c.322-3074G>A

N/A Intron Variant
RNF13 transcript variant X2 XM_047447380.1:c.322-3074…

XM_047447380.1:c.322-3074G>A

N/A Intron Variant
RNF13 transcript variant X4 XM_047447381.1:c.322-3074…

XM_047447381.1:c.322-3074G>A

N/A Intron Variant
RNF13 transcript variant X5 XM_047447382.1:c.322-3074…

XM_047447382.1:c.322-3074G>A

N/A Intron Variant
RNF13 transcript variant X6 XM_017005661.3:c. N/A Genic 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.

Not Reported in ClinVar
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
GRCh38.p14 chr 3 NC_000003.12:g.149892399= NC_000003.12:g.149892399G>A
GRCh37.p13 chr 3 NC_000003.11:g.149610186= NC_000003.11:g.149610186G>A
RNF13 transcript variant 5 NM_001378285.1:c.322-3074= NM_001378285.1:c.322-3074G>A
RNF13 transcript variant 6 NM_001378286.1:c.322-3074= NM_001378286.1:c.322-3074G>A
RNF13 transcript variant 7 NM_001378287.1:c.-46-3074= NM_001378287.1:c.-46-3074G>A
RNF13 transcript variant 8 NM_001378288.1:c.-46-3074= NM_001378288.1:c.-46-3074G>A
RNF13 transcript variant 9 NM_001378289.1:c.-46-3074= NM_001378289.1:c.-46-3074G>A
RNF13 transcript variant 10 NM_001378290.1:c.-46-3074= NM_001378290.1:c.-46-3074G>A
RNF13 transcript variant 11 NM_001378291.1:c.-72-3074= NM_001378291.1:c.-72-3074G>A
RNF13 transcript variant 1 NM_007282.4:c.322-3074= NM_007282.4:c.322-3074G>A
RNF13 transcript variant 4 NM_183381.2:c.322-3074= NM_183381.2:c.322-3074G>A
RNF13 transcript variant 4 NM_183381.3:c.322-3074= NM_183381.3:c.322-3074G>A
RNF13 transcript variant 3 NM_183383.2:c.-46-3074= NM_183383.2:c.-46-3074G>A
RNF13 transcript variant X1 XM_005247090.1:c.322-3074= XM_005247090.1:c.322-3074G>A
RNF13 transcript variant X2 XM_005247091.1:c.322-3074= XM_005247091.1:c.322-3074G>A
RNF13 transcript variant X3 XM_005247092.1:c.-46-3074= XM_005247092.1:c.-46-3074G>A
RNF13 transcript variant X3 XM_011512373.3:c.322-3074= XM_011512373.3:c.322-3074G>A
RNF13 transcript variant X1 XM_047447379.1:c.322-3074= XM_047447379.1:c.322-3074G>A
RNF13 transcript variant X2 XM_047447380.1:c.322-3074= XM_047447380.1:c.322-3074G>A
RNF13 transcript variant X4 XM_047447381.1:c.322-3074= XM_047447381.1:c.322-3074G>A
RNF13 transcript variant X5 XM_047447382.1:c.322-3074= XM_047447382.1:c.322-3074G>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#.

27 SubSNP, 10 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss239443184 Jul 15, 2010 (132)
2 GMI ss277398888 May 04, 2012 (137)
3 SSMP ss650756687 Apr 25, 2013 (138)
4 JMKIDD_LAB ss1070933994 Aug 21, 2014 (142)
5 1000GENOMES ss1306678973 Aug 21, 2014 (142)
6 JJLAB ss2021831585 Sep 14, 2016 (149)
7 HUMAN_LONGEVITY ss2256912375 Dec 20, 2016 (150)
8 SYSTEMSBIOZJU ss2625416106 Nov 08, 2017 (151)
9 GRF ss2705341532 Nov 08, 2017 (151)
10 GNOMAD ss2800616271 Nov 08, 2017 (151)
11 EVA_DECODE ss3710541804 Jul 13, 2019 (153)
12 EVA ss3760852072 Jul 13, 2019 (153)
13 KHV_HUMAN_GENOMES ss3803986736 Jul 13, 2019 (153)
14 SGDP_PRJ ss3857244005 Apr 25, 2020 (154)
15 KRGDB ss3903283076 Apr 25, 2020 (154)
16 TOPMED ss4588165073 Apr 26, 2021 (155)
17 TOMMO_GENOMICS ss5162168265 Apr 26, 2021 (155)
18 1000G_HIGH_COVERAGE ss5256480812 Oct 12, 2022 (156)
19 EVA ss5344103526 Oct 12, 2022 (156)
20 HUGCELL_USP ss5455574252 Oct 12, 2022 (156)
21 1000G_HIGH_COVERAGE ss5536157789 Oct 12, 2022 (156)
22 SANFORD_IMAGENETICS ss5633448218 Oct 12, 2022 (156)
23 TOMMO_GENOMICS ss5695215647 Oct 12, 2022 (156)
24 YY_MCH ss5804358728 Oct 12, 2022 (156)
25 EVA ss5826654601 Oct 12, 2022 (156)
26 EVA ss5871525216 Oct 12, 2022 (156)
27 EVA ss5961809527 Oct 12, 2022 (156)
28 1000Genomes NC_000003.11 - 149610186 Oct 12, 2018 (152)
29 1000Genomes_30x NC_000003.12 - 149892399 Oct 12, 2022 (156)
30 gnomAD - Genomes NC_000003.12 - 149892399 Apr 26, 2021 (155)
31 KOREAN population from KRGDB NC_000003.11 - 149610186 Apr 25, 2020 (154)
32 SGDP_PRJ NC_000003.11 - 149610186 Apr 25, 2020 (154)
33 8.3KJPN NC_000003.11 - 149610186 Apr 26, 2021 (155)
34 14KJPN NC_000003.12 - 149892399 Oct 12, 2022 (156)
35 TopMed NC_000003.12 - 149892399 Apr 26, 2021 (155)
36 A Vietnamese Genetic Variation Database NC_000003.11 - 149610186 Jul 13, 2019 (153)
37 ALFA NC_000003.12 - 149892399 Apr 26, 2021 (155)
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
ss277398888 NC_000003.10:151092875:G:A NC_000003.12:149892398:G:A (self)
17961138, 10460470, 9260985, 20137572, 2182161, ss239443184, ss650756687, ss1070933994, ss1306678973, ss2021831585, ss2625416106, ss2705341532, ss2800616271, ss3760852072, ss3857244005, ss3903283076, ss5162168265, ss5344103526, ss5633448218, ss5826654601, ss5961809527 NC_000003.11:149610185:G:A NC_000003.12:149892398:G:A (self)
23683724, 127595595, 29052751, 425542628, 5634450331, ss2256912375, ss3710541804, ss3803986736, ss4588165073, ss5256480812, ss5455574252, ss5536157789, ss5695215647, ss5804358728, ss5871525216 NC_000003.12:149892398:G:A NC_000003.12:149892398:G:A (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 rs117250923

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