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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs113224395

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr14:67432050 (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
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.035528 (9404/264690, TOPMED)
G=0.036666 (5143/140266, GnomAD)
G=0.00173 (49/28258, 14KJPN) (+ 17 more)
G=0.04402 (1138/25852, ALFA)
G=0.00155 (26/16760, 8.3KJPN)
G=0.0259 (166/6404, 1000G_30x)
G=0.0246 (123/5008, 1000G)
G=0.0469 (210/4480, Estonian)
G=0.0415 (160/3854, ALSPAC)
G=0.0442 (164/3708, TWINSUK)
G=0.0055 (16/2922, KOREAN)
G=0.0016 (3/1832, Korea1K)
G=0.039 (39/998, GoNL)
G=0.040 (24/600, NorthernSweden)
G=0.074 (16/216, Qatari)
G=0.005 (1/212, Vietnamese)
G=0.03 (1/40, GENOME_DK)
A=0.47 (14/30, SGDP_PRJ)
A=0.5 (1/2, Siberian)
G=0.5 (1/2, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
GPHN : 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 25946 A=0.95579 G=0.04421
European Sub 20496 A=0.94897 G=0.05103
African Sub 3372 A=0.9914 G=0.0086
African Others Sub 114 A=1.000 G=0.000
African American Sub 3258 A=0.9911 G=0.0089
Asian Sub 112 A=0.991 G=0.009
East Asian Sub 86 A=0.99 G=0.01
Other Asian Sub 26 A=1.00 G=0.00
Latin American 1 Sub 146 A=0.959 G=0.041
Latin American 2 Sub 610 A=0.970 G=0.030
South Asian Sub 98 A=0.93 G=0.07
Other Sub 1112 A=0.9640 G=0.0360


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 A=0.964472 G=0.035528
gnomAD - Genomes Global Study-wide 140266 A=0.963334 G=0.036666
gnomAD - Genomes European Sub 75946 A=0.95004 G=0.04996
gnomAD - Genomes African Sub 42048 A=0.99130 G=0.00870
gnomAD - Genomes American Sub 13662 A=0.95733 G=0.04267
gnomAD - Genomes Ashkenazi Jewish Sub 3322 A=0.9121 G=0.0879
gnomAD - Genomes East Asian Sub 3134 A=0.9914 G=0.0086
gnomAD - Genomes Other Sub 2154 A=0.9624 G=0.0376
14KJPN JAPANESE Study-wide 28258 A=0.99827 G=0.00173
Allele Frequency Aggregator Total Global 25852 A=0.95598 G=0.04402
Allele Frequency Aggregator European Sub 20420 A=0.94907 G=0.05093
Allele Frequency Aggregator African Sub 3372 A=0.9914 G=0.0086
Allele Frequency Aggregator Other Sub 1094 A=0.9662 G=0.0338
Allele Frequency Aggregator Latin American 2 Sub 610 A=0.970 G=0.030
Allele Frequency Aggregator Latin American 1 Sub 146 A=0.959 G=0.041
Allele Frequency Aggregator Asian Sub 112 A=0.991 G=0.009
Allele Frequency Aggregator South Asian Sub 98 A=0.93 G=0.07
8.3KJPN JAPANESE Study-wide 16760 A=0.99845 G=0.00155
1000Genomes_30x Global Study-wide 6404 A=0.9741 G=0.0259
1000Genomes_30x African Sub 1786 A=0.9994 G=0.0006
1000Genomes_30x Europe Sub 1266 A=0.9273 G=0.0727
1000Genomes_30x South Asian Sub 1202 A=0.9759 G=0.0241
1000Genomes_30x East Asian Sub 1170 A=0.9923 G=0.0077
1000Genomes_30x American Sub 980 A=0.964 G=0.036
1000Genomes Global Study-wide 5008 A=0.9754 G=0.0246
1000Genomes African Sub 1322 A=0.9992 G=0.0008
1000Genomes East Asian Sub 1008 A=0.9950 G=0.0050
1000Genomes Europe Sub 1006 A=0.9374 G=0.0626
1000Genomes South Asian Sub 978 A=0.974 G=0.026
1000Genomes American Sub 694 A=0.958 G=0.042
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.9531 G=0.0469
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.9585 G=0.0415
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.9558 G=0.0442
KOREAN population from KRGDB KOREAN Study-wide 2922 A=0.9945 G=0.0055
Korean Genome Project KOREAN Study-wide 1832 A=0.9984 G=0.0016
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.961 G=0.039
Northern Sweden ACPOP Study-wide 600 A=0.960 G=0.040
Qatari Global Study-wide 216 A=0.926 G=0.074
A Vietnamese Genetic Variation Database Global Study-wide 212 A=0.995 G=0.005
The Danish reference pan genome Danish Study-wide 40 A=0.97 G=0.03
SGDP_PRJ Global Study-wide 30 A=0.47 G=0.53
Siberian Global Study-wide 2 A=0.5 G=0.5
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 14 NC_000014.9:g.67432050A>G
GRCh37.p13 chr 14 NC_000014.8:g.67898767A>G
Gene: GPHN, gephyrin (plus strand)
Molecule type Change Amino acid[Codon] SO Term
GPHN transcript variant 2 NM_001024218.2:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant 3 NM_001377514.1:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant 4 NM_001377515.1:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant 5 NM_001377516.1:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant 6 NM_001377517.1:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant 7 NM_001377518.1:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant 8 NM_001377519.1:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant 1 NM_020806.5:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant X14 XM_047430879.1:c.1313-303…

XM_047430879.1:c.1313-303145A>G

 		N/A Intron Variant
GPHN transcript variant X1 XM_011536340.4:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant X3 XM_011536342.4:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant X5 XM_011536343.4:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant X7 XM_011536344.4:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant X9 XM_011536345.4:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant X2 XM_017020913.3:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant X4 XM_017020914.3:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant X10 XM_017020917.3:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant X11 XM_017020918.3:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant X6 XM_047430875.1:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant X8 XM_047430876.1:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant X12 XM_047430877.1:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant X13 XM_047430878.1:c. N/A Genic Downstream Transcript Variant
GPHN transcript variant X15 XM_047430880.1:c. N/A Genic Downstream 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 A= G
GRCh38.p14 chr 14 NC_000014.9:g.67432050= NC_000014.9:g.67432050A>G
GRCh37.p13 chr 14 NC_000014.8:g.67898767= NC_000014.8:g.67898767A>G
GPHN transcript variant X14 XM_047430879.1:c.1313-303145= XM_047430879.1:c.1313-303145A>G
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#.

44 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 COMPLETE_GENOMICS ss168223392 Jul 04, 2010 (132)
2 1000GENOMES ss236583907 Jul 15, 2010 (132)
3 BL ss255066506 May 09, 2011 (134)
4 EVA-GONL ss991261259 Aug 21, 2014 (142)
5 JMKIDD_LAB ss1079742172 Aug 21, 2014 (142)
6 1000GENOMES ss1351441745 Aug 21, 2014 (142)
7 EVA_GENOME_DK ss1577320700 Apr 01, 2015 (144)
8 EVA_UK10K_ALSPAC ss1631970215 Apr 01, 2015 (144)
9 EVA_UK10K_TWINSUK ss1674964248 Apr 01, 2015 (144)
10 EVA_DECODE ss1695265682 Apr 01, 2015 (144)
11 WEILL_CORNELL_DGM ss1934634482 Feb 12, 2016 (147)
12 JJLAB ss2028097436 Sep 14, 2016 (149)
13 USC_VALOUEV ss2156473002 Dec 20, 2016 (150)
14 HUMAN_LONGEVITY ss2202892270 Dec 20, 2016 (150)
15 GNOMAD ss2928947279 Nov 08, 2017 (151)
16 AFFY ss2985024431 Nov 08, 2017 (151)
17 AFFY ss2985657750 Nov 08, 2017 (151)
18 SWEGEN ss3012380043 Nov 08, 2017 (151)
19 ILLUMINA ss3021578790 Nov 08, 2017 (151)
20 CSHL ss3350857976 Nov 08, 2017 (151)
21 BIOINF_KMB_FNS_UNIBA ss3645353174 Oct 12, 2018 (152)
22 ILLUMINA ss3651972170 Oct 12, 2018 (152)
23 ILLUMINA ss3653795582 Oct 12, 2018 (152)
24 EGCUT_WGS ss3679635242 Jul 13, 2019 (153)
25 EVA_DECODE ss3696895438 Jul 13, 2019 (153)
26 ILLUMINA ss3725456859 Jul 13, 2019 (153)
27 ACPOP ss3740478741 Jul 13, 2019 (153)
28 EVA ss3752455681 Jul 13, 2019 (153)
29 KHV_HUMAN_GENOMES ss3817786302 Jul 13, 2019 (153)
30 SGDP_PRJ ss3881736681 Apr 27, 2020 (154)
31 KRGDB ss3930776481 Apr 27, 2020 (154)
32 KOGIC ss3975144556 Apr 27, 2020 (154)
33 TOPMED ss4974465482 Apr 27, 2021 (155)
34 TOMMO_GENOMICS ss5213728831 Apr 27, 2021 (155)
35 1000G_HIGH_COVERAGE ss5296607489 Oct 16, 2022 (156)
36 EVA ss5415960923 Oct 16, 2022 (156)
37 HUGCELL_USP ss5490612785 Oct 16, 2022 (156)
38 1000G_HIGH_COVERAGE ss5597083047 Oct 16, 2022 (156)
39 SANFORD_IMAGENETICS ss5656438226 Oct 16, 2022 (156)
40 TOMMO_GENOMICS ss5766674679 Oct 16, 2022 (156)
41 YY_MCH ss5814846706 Oct 16, 2022 (156)
42 EVA ss5841259955 Oct 16, 2022 (156)
43 EVA ss5901780883 Oct 16, 2022 (156)
44 EVA ss5947880835 Oct 16, 2022 (156)
45 1000Genomes NC_000014.8 - 67898767 Oct 12, 2018 (152)
46 1000Genomes_30x NC_000014.9 - 67432050 Oct 16, 2022 (156)
47 The Avon Longitudinal Study of Parents and Children NC_000014.8 - 67898767 Oct 12, 2018 (152)
48 Genetic variation in the Estonian population NC_000014.8 - 67898767 Oct 12, 2018 (152)
49 The Danish reference pan genome NC_000014.8 - 67898767 Apr 27, 2020 (154)
50 gnomAD - Genomes NC_000014.9 - 67432050 Apr 27, 2021 (155)
51 Genome of the Netherlands Release 5 NC_000014.8 - 67898767 Apr 27, 2020 (154)
52 KOREAN population from KRGDB NC_000014.8 - 67898767 Apr 27, 2020 (154)
53 Korean Genome Project NC_000014.9 - 67432050 Apr 27, 2020 (154)
54 Northern Sweden NC_000014.8 - 67898767 Jul 13, 2019 (153)
55 Qatari NC_000014.8 - 67898767 Apr 27, 2020 (154)
56 SGDP_PRJ NC_000014.8 - 67898767 Apr 27, 2020 (154)
57 Siberian NC_000014.8 - 67898767 Apr 27, 2020 (154)
58 8.3KJPN NC_000014.8 - 67898767 Apr 27, 2021 (155)
59 14KJPN NC_000014.9 - 67432050 Oct 16, 2022 (156)
60 TopMed NC_000014.9 - 67432050 Apr 27, 2021 (155)
61 UK 10K study - Twins NC_000014.8 - 67898767 Oct 12, 2018 (152)
62 A Vietnamese Genetic Variation Database NC_000014.8 - 67898767 Jul 13, 2019 (153)
63 ALFA NC_000014.9 - 67432050 Apr 27, 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
ss168223392, ss255066506, ss1695265682 NC_000014.7:66968519:A:G NC_000014.9:67432049:A:G (self)
64439214, 35802453, 25373490, 3648684, 15989247, 37953875, 13763606, 16676412, 33753661, 8989356, 71698138, 35802453, 7965018, ss236583907, ss991261259, ss1079742172, ss1351441745, ss1577320700, ss1631970215, ss1674964248, ss1934634482, ss2028097436, ss2156473002, ss2928947279, ss2985024431, ss2985657750, ss3012380043, ss3021578790, ss3350857976, ss3651972170, ss3653795582, ss3679635242, ss3740478741, ss3752455681, ss3881736681, ss3930776481, ss5213728831, ss5415960923, ss5656438226, ss5841259955, ss5947880835 NC_000014.8:67898766:A:G NC_000014.9:67432049:A:G (self)
84608982, 454365008, 31522557, 100511783, 190011141, 1574016714, ss2202892270, ss3645353174, ss3696895438, ss3725456859, ss3817786302, ss3975144556, ss4974465482, ss5296607489, ss5490612785, ss5597083047, ss5766674679, ss5814846706, ss5901780883 NC_000014.9:67432049:A:G NC_000014.9:67432049:A:G (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 rs113224395

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