Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

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.

rs199723282

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr14:73198043 (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
T>C / T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.000000 (0/142590, ALFA)
G=0.020500 (2163/105512, ExAC)
G=0.00001 (1/78690, PAGE_STUDY) (+ 3 more)
G=0.00028 (8/28258, 14KJPN)
G=0.00048 (8/16760, 8.3KJPN)
G=0.0033 (6/1822, Korea1K)
Clinical Significance
Reported in ClinVar
Gene : Consequence
PSEN1 : Missense Variant
Publications
1 citation
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 142712 T=1.000000 G=0.000000
European Sub 133768 T=1.000000 G=0.000000
African Sub 974 T=1.000 G=0.000
African Others Sub 54 T=1.00 G=0.00
African American Sub 920 T=1.000 G=0.000
Asian Sub 3234 T=1.0000 G=0.0000
East Asian Sub 2608 T=1.0000 G=0.0000
Other Asian Sub 626 T=1.000 G=0.000
Latin American 1 Sub 296 T=1.000 G=0.000
Latin American 2 Sub 338 T=1.000 G=0.000
South Asian Sub 176 T=1.000 G=0.000
Other Sub 3926 T=1.0000 G=0.0000


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
Allele Frequency Aggregator Total Global 142590 T=1.000000 G=0.000000
Allele Frequency Aggregator European Sub 133664 T=1.000000 G=0.000000
Allele Frequency Aggregator Other Sub 3922 T=1.0000 G=0.0000
Allele Frequency Aggregator Asian Sub 3234 T=1.0000 G=0.0000
Allele Frequency Aggregator African Sub 960 T=1.000 G=0.000
Allele Frequency Aggregator Latin American 2 Sub 338 T=1.000 G=0.000
Allele Frequency Aggregator Latin American 1 Sub 296 T=1.000 G=0.000
Allele Frequency Aggregator South Asian Sub 176 T=1.000 G=0.000
ExAC Global Study-wide 105512 T=0.979500 G=0.020500
ExAC Europe Sub 61996 T=0.97319 G=0.02681
ExAC Asian Sub 23628 T=0.99687 G=0.00313
ExAC American Sub 10764 T=0.99638 G=0.00362
ExAC African Sub 8368 T=0.9566 G=0.0434
ExAC Other Sub 756 T=0.967 G=0.033
The PAGE Study Global Study-wide 78690 T=0.99999 G=0.00001
The PAGE Study AfricanAmerican Sub 32512 T=0.99997 G=0.00003
The PAGE Study Mexican Sub 10808 T=1.00000 G=0.00000
The PAGE Study Asian Sub 8316 T=1.0000 G=0.0000
The PAGE Study PuertoRican Sub 7916 T=1.0000 G=0.0000
The PAGE Study NativeHawaiian Sub 4534 T=1.0000 G=0.0000
The PAGE Study Cuban Sub 4230 T=1.0000 G=0.0000
The PAGE Study Dominican Sub 3828 T=1.0000 G=0.0000
The PAGE Study CentralAmerican Sub 2450 T=1.0000 G=0.0000
The PAGE Study SouthAmerican Sub 1982 T=1.0000 G=0.0000
The PAGE Study NativeAmerican Sub 1260 T=1.0000 G=0.0000
The PAGE Study SouthAsian Sub 854 T=1.000 G=0.000
14KJPN JAPANESE Study-wide 28258 T=0.99972 G=0.00028
8.3KJPN JAPANESE Study-wide 16760 T=0.99952 G=0.00048
Korean Genome Project KOREAN Study-wide 1822 T=0.9967 G=0.0033
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.73198043T>C
GRCh38.p14 chr 14 NC_000014.9:g.73198043T>G
GRCh37.p13 chr 14 NC_000014.8:g.73664751T>C
GRCh37.p13 chr 14 NC_000014.8:g.73664751T>G
PSEN1 RefSeqGene (LRG_224) NG_007386.2:g.66573T>C
PSEN1 RefSeqGene (LRG_224) NG_007386.2:g.66573T>G
Gene: PSEN1, presenilin 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
PSEN1 transcript variant 1 NM_000021.4:c.782T>C V [GTT] > A [GCT] Coding Sequence Variant
presenilin-1 isoform I-467 NP_000012.1:p.Val261Ala V (Val) > A (Ala) Missense Variant
PSEN1 transcript variant 1 NM_000021.4:c.782T>G V [GTT] > G [GGT] Coding Sequence Variant
presenilin-1 isoform I-467 NP_000012.1:p.Val261Gly V (Val) > G (Gly) Missense Variant
PSEN1 transcript variant 2 NM_007318.3:c.770T>C V [GTT] > A [GCT] Coding Sequence Variant
presenilin-1 isoform I-463 NP_015557.2:p.Val257Ala V (Val) > A (Ala) Missense Variant
PSEN1 transcript variant 2 NM_007318.3:c.770T>G V [GTT] > G [GGT] Coding Sequence Variant
presenilin-1 isoform I-463 NP_015557.2:p.Val257Gly V (Val) > G (Gly) Missense Variant
PSEN1 transcript variant X1 XM_005267864.4:c.782T>C V [GTT] > A [GCT] Coding Sequence Variant
presenilin-1 isoform X1 XP_005267921.1:p.Val261Ala V (Val) > A (Ala) Missense Variant
PSEN1 transcript variant X1 XM_005267864.4:c.782T>G V [GTT] > G [GGT] Coding Sequence Variant
presenilin-1 isoform X1 XP_005267921.1:p.Val261Gly V (Val) > G (Gly) Missense Variant
PSEN1 transcript variant X2 XM_047431600.1:c.782T>C V [GTT] > A [GCT] Coding Sequence Variant
presenilin-1 isoform X1 XP_047287556.1:p.Val261Ala V (Val) > A (Ala) Missense Variant
PSEN1 transcript variant X2 XM_047431600.1:c.782T>G V [GTT] > G [GGT] Coding Sequence Variant
presenilin-1 isoform X1 XP_047287556.1:p.Val261Gly V (Val) > G (Gly) Missense Variant
PSEN1 transcript variant X3 XM_047431601.1:c.782T>C V [GTT] > A [GCT] Coding Sequence Variant
presenilin-1 isoform X1 XP_047287557.1:p.Val261Ala V (Val) > A (Ala) Missense Variant
PSEN1 transcript variant X3 XM_047431601.1:c.782T>G V [GTT] > G [GGT] Coding Sequence Variant
presenilin-1 isoform X1 XP_047287557.1:p.Val261Gly V (Val) > G (Gly) Missense Variant
PSEN1 transcript variant X4 XM_011536972.3:c.782T>C V [GTT] > A [GCT] Coding Sequence Variant
presenilin-1 isoform X1 XP_011535274.1:p.Val261Ala V (Val) > A (Ala) Missense Variant
PSEN1 transcript variant X4 XM_011536972.3:c.782T>G V [GTT] > G [GGT] Coding Sequence Variant
presenilin-1 isoform X1 XP_011535274.1:p.Val261Gly V (Val) > G (Gly) Missense Variant
PSEN1 transcript variant X5 XM_005267866.3:c.770T>C V [GTT] > A [GCT] Coding Sequence Variant
presenilin-1 isoform X2 XP_005267923.1:p.Val257Ala V (Val) > A (Ala) Missense Variant
PSEN1 transcript variant X5 XM_005267866.3:c.770T>G V [GTT] > G [GGT] Coding Sequence Variant
presenilin-1 isoform X2 XP_005267923.1:p.Val257Gly V (Val) > G (Gly) Missense Variant
PSEN1 transcript variant X6 XM_011536974.3:c.770T>C V [GTT] > A [GCT] Coding Sequence Variant
presenilin-1 isoform X2 XP_011535276.1:p.Val257Ala V (Val) > A (Ala) Missense Variant
PSEN1 transcript variant X6 XM_011536974.3:c.770T>G V [GTT] > G [GGT] Coding Sequence Variant
presenilin-1 isoform X2 XP_011535276.1:p.Val257Gly V (Val) > G (Gly) Missense Variant
PSEN1 transcript variant X7 XM_011536973.3:c.770T>C V [GTT] > A [GCT] Coding Sequence Variant
presenilin-1 isoform X2 XP_011535275.1:p.Val257Ala V (Val) > A (Ala) Missense Variant
PSEN1 transcript variant X7 XM_011536973.3:c.770T>G V [GTT] > G [GGT] Coding Sequence Variant
presenilin-1 isoform X2 XP_011535275.1:p.Val257Gly V (Val) > G (Gly) Missense Variant
PSEN1 transcript variant X8 XM_047431602.1:c.770T>C V [GTT] > A [GCT] Coding Sequence Variant
presenilin-1 isoform X2 XP_047287558.1:p.Val257Ala V (Val) > A (Ala) Missense Variant
PSEN1 transcript variant X8 XM_047431602.1:c.770T>G V [GTT] > G [GGT] Coding Sequence Variant
presenilin-1 isoform X2 XP_047287558.1:p.Val257Gly V (Val) > G (Gly) Missense 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.

Allele: C (allele ID: 1167851 )
ClinVar Accession Disease Names Clinical Significance
RCV001810075.1 Alzheimer disease 3 Likely-Pathogenic
Allele: G (allele ID: 189959 )
ClinVar Accession Disease Names Clinical Significance
RCV000172775.1 not specified Benign
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 T= C G
GRCh38.p14 chr 14 NC_000014.9:g.73198043= NC_000014.9:g.73198043T>C NC_000014.9:g.73198043T>G
GRCh37.p13 chr 14 NC_000014.8:g.73664751= NC_000014.8:g.73664751T>C NC_000014.8:g.73664751T>G
PSEN1 RefSeqGene (LRG_224) NG_007386.2:g.66573= NG_007386.2:g.66573T>C NG_007386.2:g.66573T>G
PSEN1 transcript variant 1 NM_000021.4:c.782= NM_000021.4:c.782T>C NM_000021.4:c.782T>G
PSEN1 transcript variant 1 NM_000021.3:c.782= NM_000021.3:c.782T>C NM_000021.3:c.782T>G
PSEN1 transcript variant 2 NM_007318.3:c.770= NM_007318.3:c.770T>C NM_007318.3:c.770T>G
PSEN1 transcript variant 2 NM_007318.2:c.770= NM_007318.2:c.770T>C NM_007318.2:c.770T>G
PSEN1 transcript variant X1 XM_005267864.4:c.782= XM_005267864.4:c.782T>C XM_005267864.4:c.782T>G
PSEN1 transcript variant X1 XM_005267864.3:c.782= XM_005267864.3:c.782T>C XM_005267864.3:c.782T>G
PSEN1 transcript variant X1 XM_005267864.2:c.782= XM_005267864.2:c.782T>C XM_005267864.2:c.782T>G
PSEN1 transcript variant X1 XM_005267864.1:c.782= XM_005267864.1:c.782T>C XM_005267864.1:c.782T>G
PSEN1 transcript variant X6 XM_011536974.3:c.770= XM_011536974.3:c.770T>C XM_011536974.3:c.770T>G
PSEN1 transcript variant X4 XM_011536974.2:c.770= XM_011536974.2:c.770T>C XM_011536974.2:c.770T>G
PSEN1 transcript variant X5 XM_011536974.1:c.770= XM_011536974.1:c.770T>C XM_011536974.1:c.770T>G
PSEN1 transcript variant X4 XM_011536972.3:c.782= XM_011536972.3:c.782T>C XM_011536972.3:c.782T>G
PSEN1 transcript variant X2 XM_011536972.2:c.782= XM_011536972.2:c.782T>C XM_011536972.2:c.782T>G
PSEN1 transcript variant X3 XM_011536972.1:c.782= XM_011536972.1:c.782T>C XM_011536972.1:c.782T>G
PSEN1 transcript variant X7 XM_011536973.3:c.770= XM_011536973.3:c.770T>C XM_011536973.3:c.770T>G
PSEN1 transcript variant X5 XM_011536973.2:c.770= XM_011536973.2:c.770T>C XM_011536973.2:c.770T>G
PSEN1 transcript variant X6 XM_011536973.1:c.770= XM_011536973.1:c.770T>C XM_011536973.1:c.770T>G
PSEN1 transcript variant X5 XM_005267866.3:c.770= XM_005267866.3:c.770T>C XM_005267866.3:c.770T>G
PSEN1 transcript variant X3 XM_005267866.2:c.770= XM_005267866.2:c.770T>C XM_005267866.2:c.770T>G
PSEN1 transcript variant X4 XM_005267866.1:c.770= XM_005267866.1:c.770T>C XM_005267866.1:c.770T>G
PSEN1 transcript variant X2 XM_047431600.1:c.782= XM_047431600.1:c.782T>C XM_047431600.1:c.782T>G
PSEN1 transcript variant X3 XM_047431601.1:c.782= XM_047431601.1:c.782T>C XM_047431601.1:c.782T>G
PSEN1 transcript variant X8 XM_047431602.1:c.770= XM_047431602.1:c.770T>C XM_047431602.1:c.770T>G
PSEN1 transcript variant I-374. NM_007319.1:c.770= NM_007319.1:c.770T>C NM_007319.1:c.770T>G
presenilin-1 isoform I-467 NP_000012.1:p.Val261= NP_000012.1:p.Val261Ala NP_000012.1:p.Val261Gly
presenilin-1 isoform I-463 NP_015557.2:p.Val257= NP_015557.2:p.Val257Ala NP_015557.2:p.Val257Gly
presenilin-1 isoform X1 XP_005267921.1:p.Val261= XP_005267921.1:p.Val261Ala XP_005267921.1:p.Val261Gly
presenilin-1 isoform X2 XP_011535276.1:p.Val257= XP_011535276.1:p.Val257Ala XP_011535276.1:p.Val257Gly
presenilin-1 isoform X1 XP_011535274.1:p.Val261= XP_011535274.1:p.Val261Ala XP_011535274.1:p.Val261Gly
presenilin-1 isoform X2 XP_011535275.1:p.Val257= XP_011535275.1:p.Val257Ala XP_011535275.1:p.Val257Gly
presenilin-1 isoform X2 XP_005267923.1:p.Val257= XP_005267923.1:p.Val257Ala XP_005267923.1:p.Val257Gly
presenilin-1 isoform X1 XP_047287556.1:p.Val261= XP_047287556.1:p.Val261Ala XP_047287556.1:p.Val261Gly
presenilin-1 isoform X1 XP_047287557.1:p.Val261= XP_047287557.1:p.Val261Ala XP_047287557.1:p.Val261Gly
presenilin-1 isoform X2 XP_047287558.1:p.Val257= XP_047287558.1:p.Val257Ala XP_047287558.1:p.Val257Gly
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#.

30 SubSNP, 6 Frequency, 2 ClinVar submissions
No Submitter Submission ID Date (Build)
1 GSK-GENETICS ss491248109 May 04, 2012 (137)
2 EXOME_CHIP ss491486941 May 04, 2012 (137)
3 CLINSEQ_SNP ss491689968 May 04, 2012 (137)
4 ILLUMINA ss780702795 Sep 08, 2015 (146)
5 ILLUMINA ss783377129 Sep 08, 2015 (146)
6 EVA_EXAC ss1691546769 Apr 01, 2015 (144)
7 ILLUMINA ss1752141386 Sep 08, 2015 (146)
8 ILLUMINA ss1917890308 Feb 12, 2016 (147)
9 ILLUMINA ss1946380686 Feb 12, 2016 (147)
10 ILLUMINA ss1959565599 Feb 12, 2016 (147)
11 GRF ss2700927837 Nov 08, 2017 (151)
12 ILLUMINA ss2710804741 Nov 08, 2017 (151)
13 GNOMAD ss2740816473 Nov 08, 2017 (151)
14 AFFY ss2985025715 Nov 08, 2017 (151)
15 ILLUMINA ss3625662362 Oct 12, 2018 (152)
16 ILLUMINA ss3627253971 Oct 12, 2018 (152)
17 ILLUMINA ss3634583806 Oct 12, 2018 (152)
18 ILLUMINA ss3640291133 Oct 12, 2018 (152)
19 ILLUMINA ss3644633811 Oct 12, 2018 (152)
20 ILLUMINA ss3653796859 Oct 12, 2018 (152)
21 ILLUMINA ss3744413573 Jul 13, 2019 (153)
22 ILLUMINA ss3744884424 Jul 13, 2019 (153)
23 PAGE_CC ss3771798666 Jul 13, 2019 (153)
24 ILLUMINA ss3772383209 Jul 13, 2019 (153)
25 KOGIC ss3975228408 Apr 27, 2020 (154)
26 EVA ss3986064895 Apr 26, 2021 (155)
27 TOMMO_GENOMICS ss5213908770 Apr 26, 2021 (155)
28 TOMMO_GENOMICS ss5766907581 Oct 16, 2022 (156)
29 EVA ss5847725787 Oct 16, 2022 (156)
30 EVA ss5947965132 Oct 16, 2022 (156)
31 ExAC NC_000014.8 - 73664751 Oct 12, 2018 (152)
32 Korean Genome Project NC_000014.9 - 73198043 Apr 27, 2020 (154)
33 The PAGE Study NC_000014.9 - 73198043 Jul 13, 2019 (153)
34 8.3KJPN NC_000014.8 - 73664751 Apr 26, 2021 (155)
35 14KJPN NC_000014.9 - 73198043 Oct 16, 2022 (156)
36 ALFA NC_000014.9 - 73198043 Apr 26, 2021 (155)
37 ClinVar RCV000172775.1 Oct 12, 2018 (152)
38 ClinVar RCV001810075.1 Oct 16, 2022 (156)
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
RCV001810075.1 NC_000014.9:73198042:T:C NC_000014.9:73198042:T:C
ss491248109, ss491689968 NC_000014.7:72734503:T:G NC_000014.9:73198042:T:G (self)
1897201, 71878077, ss491486941, ss780702795, ss783377129, ss1691546769, ss1752141386, ss1917890308, ss1946380686, ss1959565599, ss2700927837, ss2710804741, ss2740816473, ss2985025715, ss3625662362, ss3627253971, ss3634583806, ss3640291133, ss3644633811, ss3653796859, ss3744413573, ss3744884424, ss3772383209, ss3986064895, ss5213908770, ss5847725787, ss5947965132 NC_000014.8:73664750:T:G NC_000014.9:73198042:T:G (self)
RCV000172775.1, 31606409, 1020135, 100744685, 13034406440, ss3771798666, ss3975228408, ss5766907581 NC_000014.9:73198042:T:G NC_000014.9:73198042:T:G (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

1 citation for rs199723282
PMID Title Author Year Journal
23861362 Interpreting secondary cardiac disease variants in an exome cohort. Ng D et al. 2013 Circulation. Cardiovascular genetics
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