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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.

rs72719138

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr14:67411481 (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
C>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.014734 (3900/264690, TOPMED)
A=0.015898 (2228/140144, GnomAD)
A=0.01810 (342/18890, ALFA) (+ 12 more)
A=0.0108 (69/6404, 1000G_30x)
A=0.0100 (50/5008, 1000G)
A=0.0208 (93/4480, Estonian)
A=0.0241 (93/3854, ALSPAC)
A=0.0173 (64/3708, TWINSUK)
A=0.0000 (0/2922, KOREAN)
A=0.033 (33/998, GoNL)
A=0.005 (3/600, NorthernSweden)
A=0.019 (4/216, Qatari)
A=0.03 (1/40, GENOME_DK)
C=0.50 (12/24, SGDP_PRJ)
A=0.50 (12/24, 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 C=0.98190 A=0.01810
European Sub 14286 C=0.97956 A=0.02044
African Sub 2946 C=0.9936 A=0.0064
African Others Sub 114 C=1.000 A=0.000
African American Sub 2832 C=0.9933 A=0.0067
Asian Sub 112 C=1.000 A=0.000
East Asian Sub 86 C=1.00 A=0.00
Other Asian Sub 26 C=1.00 A=0.00
Latin American 1 Sub 146 C=0.979 A=0.021
Latin American 2 Sub 610 C=0.989 A=0.011
South Asian Sub 98 C=0.96 A=0.04
Other Sub 692 C=0.975 A=0.025


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 C=0.985266 A=0.014734
gnomAD - Genomes Global Study-wide 140144 C=0.984102 A=0.015898
gnomAD - Genomes European Sub 75892 C=0.97881 A=0.02119
gnomAD - Genomes African Sub 42000 C=0.99140 A=0.00860
gnomAD - Genomes American Sub 13648 C=0.98908 A=0.01092
gnomAD - Genomes Ashkenazi Jewish Sub 3320 C=0.9750 A=0.0250
gnomAD - Genomes East Asian Sub 3132 C=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2152 C=0.9875 A=0.0125
Allele Frequency Aggregator Total Global 18890 C=0.98190 A=0.01810
Allele Frequency Aggregator European Sub 14286 C=0.97956 A=0.02044
Allele Frequency Aggregator African Sub 2946 C=0.9936 A=0.0064
Allele Frequency Aggregator Other Sub 692 C=0.975 A=0.025
Allele Frequency Aggregator Latin American 2 Sub 610 C=0.989 A=0.011
Allele Frequency Aggregator Latin American 1 Sub 146 C=0.979 A=0.021
Allele Frequency Aggregator Asian Sub 112 C=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 98 C=0.96 A=0.04
1000Genomes_30x Global Study-wide 6404 C=0.9892 A=0.0108
1000Genomes_30x African Sub 1786 C=0.9933 A=0.0067
1000Genomes_30x Europe Sub 1266 C=0.9787 A=0.0213
1000Genomes_30x South Asian Sub 1202 C=0.9925 A=0.0075
1000Genomes_30x East Asian Sub 1170 C=0.9991 A=0.0009
1000Genomes_30x American Sub 980 C=0.980 A=0.020
1000Genomes Global Study-wide 5008 C=0.9900 A=0.0100
1000Genomes African Sub 1322 C=0.9932 A=0.0068
1000Genomes East Asian Sub 1008 C=0.9990 A=0.0010
1000Genomes Europe Sub 1006 C=0.9821 A=0.0179
1000Genomes South Asian Sub 978 C=0.992 A=0.008
1000Genomes American Sub 694 C=0.980 A=0.020
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.9792 A=0.0208
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9759 A=0.0241
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.9827 A=0.0173
KOREAN population from KRGDB KOREAN Study-wide 2922 C=1.0000 A=0.0000
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.967 A=0.033
Northern Sweden ACPOP Study-wide 600 C=0.995 A=0.005
Qatari Global Study-wide 216 C=0.981 A=0.019
The Danish reference pan genome Danish Study-wide 40 C=0.97 A=0.03
SGDP_PRJ Global Study-wide 24 C=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 14 NC_000014.9:g.67411481C>A
GRCh37.p13 chr 14 NC_000014.8:g.67878198C>A
Gene: PLEK2, pleckstrin 2 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
PLEK2 transcript NM_016445.3:c.42+537G>T N/A Intron Variant
PLEK2 transcript variant X1 XM_047431262.1:c.42+537G>T N/A Intron Variant
PLEK2 transcript variant X2 XM_047431263.1:c.-413+537…

XM_047431263.1:c.-413+537G>T

 		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.1313-323…

XM_047430879.1:c.1313-323714C>A

 		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 C= A
GRCh38.p14 chr 14 NC_000014.9:g.67411481= NC_000014.9:g.67411481C>A
GRCh37.p13 chr 14 NC_000014.8:g.67878198= NC_000014.8:g.67878198C>A
PLEK2 transcript NM_016445.1:c.42+537= NM_016445.1:c.42+537G>T
PLEK2 transcript NM_016445.3:c.42+537= NM_016445.3:c.42+537G>T
GPHN transcript variant X14 XM_047430879.1:c.1313-323714= XM_047430879.1:c.1313-323714C>A
PLEK2 transcript variant X1 XM_047431262.1:c.42+537= XM_047431262.1:c.42+537G>T
PLEK2 transcript variant X2 XM_047431263.1:c.-413+537= XM_047431263.1:c.-413+537G>T
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#.

35 SubSNP, 14 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss108418675 Feb 13, 2009 (130)
2 1000GENOMES ss226624924 Jul 14, 2010 (132)
3 1000GENOMES ss236583851 Jul 15, 2010 (132)
4 TISHKOFF ss564157780 Apr 25, 2013 (138)
5 SSMP ss659846197 Apr 25, 2013 (138)
6 EVA-GONL ss991261111 Aug 21, 2014 (142)
7 JMKIDD_LAB ss1079742063 Aug 21, 2014 (142)
8 1000GENOMES ss1351441182 Aug 21, 2014 (142)
9 EVA_GENOME_DK ss1577320628 Apr 01, 2015 (144)
10 EVA_UK10K_ALSPAC ss1631969904 Apr 01, 2015 (144)
11 EVA_UK10K_TWINSUK ss1674963937 Apr 01, 2015 (144)
12 EVA_DECODE ss1695265542 Apr 01, 2015 (144)
13 WEILL_CORNELL_DGM ss1934634324 Feb 12, 2016 (147)
14 JJLAB ss2028097343 Sep 14, 2016 (149)
15 HUMAN_LONGEVITY ss2202891032 Dec 20, 2016 (150)
16 GNOMAD ss2928945654 Nov 08, 2017 (151)
17 SWEGEN ss3012379819 Nov 08, 2017 (151)
18 EGCUT_WGS ss3679634978 Jul 13, 2019 (153)
19 EVA_DECODE ss3696895182 Jul 13, 2019 (153)
20 ACPOP ss3740478619 Jul 13, 2019 (153)
21 EVA ss3752455510 Jul 13, 2019 (153)
22 KHV_HUMAN_GENOMES ss3817786148 Jul 13, 2019 (153)
23 EVA ss3833974587 Apr 27, 2020 (154)
24 SGDP_PRJ ss3881736433 Apr 27, 2020 (154)
25 KRGDB ss3930776207 Apr 27, 2020 (154)
26 TOPMED ss4974460532 Apr 27, 2021 (155)
27 1000G_HIGH_COVERAGE ss5296606985 Oct 16, 2022 (156)
28 EVA ss5415960001 Oct 16, 2022 (156)
29 HUGCELL_USP ss5490612367 Oct 16, 2022 (156)
30 EVA ss5511282276 Oct 16, 2022 (156)
31 1000G_HIGH_COVERAGE ss5597082301 Oct 16, 2022 (156)
32 SANFORD_IMAGENETICS ss5656437970 Oct 16, 2022 (156)
33 EVA ss5841259757 Oct 16, 2022 (156)
34 EVA ss5901780300 Oct 16, 2022 (156)
35 EVA ss5947880568 Oct 16, 2022 (156)
36 1000Genomes NC_000014.8 - 67878198 Oct 12, 2018 (152)
37 1000Genomes_30x NC_000014.9 - 67411481 Oct 16, 2022 (156)
38 The Avon Longitudinal Study of Parents and Children NC_000014.8 - 67878198 Oct 12, 2018 (152)
39 Genetic variation in the Estonian population NC_000014.8 - 67878198 Oct 12, 2018 (152)
40 The Danish reference pan genome NC_000014.8 - 67878198 Apr 27, 2020 (154)
41 gnomAD - Genomes NC_000014.9 - 67411481 Apr 27, 2021 (155)
42 Genome of the Netherlands Release 5 NC_000014.8 - 67878198 Apr 27, 2020 (154)
43 KOREAN population from KRGDB NC_000014.8 - 67878198 Apr 27, 2020 (154)
44 Northern Sweden NC_000014.8 - 67878198 Jul 13, 2019 (153)
45 Qatari NC_000014.8 - 67878198 Apr 27, 2020 (154)
46 SGDP_PRJ NC_000014.8 - 67878198 Apr 27, 2020 (154)
47 TopMed NC_000014.9 - 67411481 Apr 27, 2021 (155)
48 UK 10K study - Twins NC_000014.8 - 67878198 Oct 12, 2018 (152)
49 ALFA NC_000014.9 - 67411481 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
ss108418675, ss1695265542 NC_000014.7:66947950:C:A NC_000014.9:67411480:C:A (self)
64438631, 35802118, 25373226, 3648615, 15989104, 37953601, 13763484, 16676254, 33753413, 35802118, ss226624924, ss236583851, ss564157780, ss659846197, ss991261111, ss1079742063, ss1351441182, ss1577320628, ss1631969904, ss1674963937, ss1934634324, ss2028097343, ss2928945654, ss3012379819, ss3679634978, ss3740478619, ss3752455510, ss3833974587, ss3881736433, ss3930776207, ss5415960001, ss5511282276, ss5656437970, ss5841259757, ss5947880568 NC_000014.8:67878197:C:A NC_000014.9:67411480:C:A (self)
84608236, 454360924, 190006191, 2666052195, ss2202891032, ss3696895182, ss3817786148, ss4974460532, ss5296606985, ss5490612367, ss5597082301, ss5901780300 NC_000014.9:67411480:C:A NC_000014.9:67411480:C: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 rs72719138

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