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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.

rs74764953

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr14:67400056 (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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.011432 (3026/264690, TOPMED)
T=0.012079 (1693/140158, GnomAD)
T=0.01350 (255/18890, ALFA) (+ 10 more)
T=0.0073 (47/6404, 1000G_30x)
T=0.0068 (34/5008, 1000G)
T=0.0165 (74/4480, Estonian)
T=0.0138 (53/3854, ALSPAC)
T=0.0216 (80/3708, TWINSUK)
T=0.0005 (1/1832, Korea1K)
T=0.018 (18/998, GoNL)
T=0.008 (5/600, NorthernSweden)
T=0.005 (1/216, Qatari)
G=0.39 (7/18, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
GPHN : Intron Variant
PLEK2 : 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 18890 G=0.98650 T=0.01350
European Sub 14286 G=0.98418 T=0.01582
African Sub 2946 G=0.9980 T=0.0020
African Others Sub 114 G=1.000 T=0.000
African American Sub 2832 G=0.9979 T=0.0021
Asian Sub 112 G=1.000 T=0.000
East Asian Sub 86 G=1.00 T=0.00
Other Asian Sub 26 G=1.00 T=0.00
Latin American 1 Sub 146 G=0.966 T=0.034
Latin American 2 Sub 610 G=0.987 T=0.013
South Asian Sub 98 G=1.00 T=0.00
Other Sub 692 G=0.986 T=0.014


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=0.988568 T=0.011432
gnomAD - Genomes Global Study-wide 140158 G=0.987921 T=0.012079
gnomAD - Genomes European Sub 75914 G=0.98203 T=0.01797
gnomAD - Genomes African Sub 41998 G=0.99693 T=0.00307
gnomAD - Genomes American Sub 13642 G=0.98871 T=0.01129
gnomAD - Genomes Ashkenazi Jewish Sub 3322 G=0.9958 T=0.0042
gnomAD - Genomes East Asian Sub 3132 G=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2150 G=0.9851 T=0.0149
Allele Frequency Aggregator Total Global 18890 G=0.98650 T=0.01350
Allele Frequency Aggregator European Sub 14286 G=0.98418 T=0.01582
Allele Frequency Aggregator African Sub 2946 G=0.9980 T=0.0020
Allele Frequency Aggregator Other Sub 692 G=0.986 T=0.014
Allele Frequency Aggregator Latin American 2 Sub 610 G=0.987 T=0.013
Allele Frequency Aggregator Latin American 1 Sub 146 G=0.966 T=0.034
Allele Frequency Aggregator Asian Sub 112 G=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 98 G=1.00 T=0.00
1000Genomes_30x Global Study-wide 6404 G=0.9927 T=0.0073
1000Genomes_30x African Sub 1786 G=1.0000 T=0.0000
1000Genomes_30x Europe Sub 1266 G=0.9803 T=0.0197
1000Genomes_30x South Asian Sub 1202 G=0.9950 T=0.0050
1000Genomes_30x East Asian Sub 1170 G=1.0000 T=0.0000
1000Genomes_30x American Sub 980 G=0.984 T=0.016
1000Genomes Global Study-wide 5008 G=0.9932 T=0.0068
1000Genomes African Sub 1322 G=1.0000 T=0.0000
1000Genomes East Asian Sub 1008 G=1.0000 T=0.0000
1000Genomes Europe Sub 1006 G=0.9831 T=0.0169
1000Genomes South Asian Sub 978 G=0.995 T=0.005
1000Genomes American Sub 694 G=0.983 T=0.017
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.9835 T=0.0165
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.9862 T=0.0138
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.9784 T=0.0216
Korean Genome Project KOREAN Study-wide 1832 G=0.9995 T=0.0005
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.982 T=0.018
Northern Sweden ACPOP Study-wide 600 G=0.992 T=0.008
Qatari Global Study-wide 216 G=0.995 T=0.005
SGDP_PRJ Global Study-wide 18 G=0.39 T=0.61
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.67400056G>T
GRCh37.p13 chr 14 NC_000014.8:g.67866773G>T
Gene: PLEK2, pleckstrin 2 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
PLEK2 transcript NM_016445.3:c.43-2230C>A N/A Intron Variant
PLEK2 transcript variant X1 XM_047431262.1:c.43-2230C…

XM_047431262.1:c.43-2230C>A

 		N/A Intron Variant
PLEK2 transcript variant X2 XM_047431263.1:c.-412-200…

XM_047431263.1:c.-412-2001C>A

 		N/A Intron Variant
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.1313-335…

XM_047430879.1:c.1313-335139G>T

 		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 G= T
GRCh38.p14 chr 14 NC_000014.9:g.67400056= NC_000014.9:g.67400056G>T
GRCh37.p13 chr 14 NC_000014.8:g.67866773= NC_000014.8:g.67866773G>T
PLEK2 transcript NM_016445.1:c.43-2230= NM_016445.1:c.43-2230C>A
PLEK2 transcript NM_016445.3:c.43-2230= NM_016445.3:c.43-2230C>A
GPHN transcript variant X14 XM_047430879.1:c.1313-335139= XM_047430879.1:c.1313-335139G>T
PLEK2 transcript variant X1 XM_047431262.1:c.43-2230= XM_047431262.1:c.43-2230C>A
PLEK2 transcript variant X2 XM_047431263.1:c.-412-2001= XM_047431263.1:c.-412-2001C>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#.

28 SubSNP, 13 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss236583827 Jul 15, 2010 (132)
2 SSMP ss659846141 Apr 25, 2013 (138)
3 EVA-GONL ss991261047 Aug 21, 2014 (142)
4 1000GENOMES ss1351440916 Aug 21, 2014 (142)
5 EVA_UK10K_ALSPAC ss1631969739 Apr 01, 2015 (144)
6 EVA_UK10K_TWINSUK ss1674963772 Apr 01, 2015 (144)
7 EVA_DECODE ss1695265462 Apr 01, 2015 (144)
8 WEILL_CORNELL_DGM ss1934634258 Feb 12, 2016 (147)
9 JJLAB ss2028097300 Sep 14, 2016 (149)
10 HUMAN_LONGEVITY ss2202890427 Dec 20, 2016 (150)
11 GNOMAD ss2928944865 Nov 08, 2017 (151)
12 SWEGEN ss3012379708 Nov 08, 2017 (151)
13 CSHL ss3350857895 Nov 08, 2017 (151)
14 EGCUT_WGS ss3679634875 Jul 13, 2019 (153)
15 EVA_DECODE ss3696895057 Jul 13, 2019 (153)
16 ACPOP ss3740478560 Jul 13, 2019 (153)
17 SGDP_PRJ ss3881736306 Apr 27, 2020 (154)
18 KOGIC ss3975144085 Apr 27, 2020 (154)
19 TOPMED ss4974458084 Apr 27, 2021 (155)
20 1000G_HIGH_COVERAGE ss5296606747 Oct 16, 2022 (156)
21 EVA ss5415959548 Oct 16, 2022 (156)
22 HUGCELL_USP ss5490612129 Oct 16, 2022 (156)
23 1000G_HIGH_COVERAGE ss5597081937 Oct 16, 2022 (156)
24 SANFORD_IMAGENETICS ss5656437842 Oct 16, 2022 (156)
25 EVA ss5841259665 Oct 16, 2022 (156)
26 EVA ss5851080450 Oct 16, 2022 (156)
27 EVA ss5901780025 Oct 16, 2022 (156)
28 EVA ss5947880428 Oct 16, 2022 (156)
29 1000Genomes NC_000014.8 - 67866773 Oct 12, 2018 (152)
30 1000Genomes_30x NC_000014.9 - 67400056 Oct 16, 2022 (156)
31 The Avon Longitudinal Study of Parents and Children NC_000014.8 - 67866773 Oct 12, 2018 (152)
32 Genetic variation in the Estonian population NC_000014.8 - 67866773 Oct 12, 2018 (152)
33 gnomAD - Genomes NC_000014.9 - 67400056 Apr 27, 2021 (155)
34 Genome of the Netherlands Release 5 NC_000014.8 - 67866773 Apr 27, 2020 (154)
35 Korean Genome Project NC_000014.9 - 67400056 Apr 27, 2020 (154)
36 Northern Sweden NC_000014.8 - 67866773 Jul 13, 2019 (153)
37 Qatari NC_000014.8 - 67866773 Apr 27, 2020 (154)
38 SGDP_PRJ NC_000014.8 - 67866773 Apr 27, 2020 (154)
39 TopMed NC_000014.9 - 67400056 Apr 27, 2021 (155)
40 UK 10K study - Twins NC_000014.8 - 67866773 Oct 12, 2018 (152)
41 ALFA NC_000014.9 - 67400056 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
ss1695265462 NC_000014.7:66936525:G:T NC_000014.9:67400055:G:T (self)
64438361, 35801939, 25373123, 15989042, 13763425, 16676188, 33753286, 35801939, ss236583827, ss659846141, ss991261047, ss1351440916, ss1631969739, ss1674963772, ss1934634258, ss2028097300, ss2928944865, ss3012379708, ss3350857895, ss3679634875, ss3740478560, ss3881736306, ss5415959548, ss5656437842, ss5841259665, ss5947880428 NC_000014.8:67866772:G:T NC_000014.9:67400055:G:T (self)
84607872, 454358810, 31522086, 190003743, 3430762267, ss2202890427, ss3696895057, ss3975144085, ss4974458084, ss5296606747, ss5490612129, ss5597081937, ss5851080450, ss5901780025 NC_000014.9:67400055:G:T NC_000014.9:67400055: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 rs74764953

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