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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.

rs201662530

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr9:136514511 (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 / C>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000159 (42/264690, TOPMED)
T=0.000042 (8/190032, GnomAD_exome)
T=0.000128 (18/140292, GnomAD) (+ 6 more)
T=0.00004 (3/75762, ALFA)
T=0.00004 (1/28258, 14KJPN)
T=0.00014 (4/27838, ExAC)
T=0.00041 (5/12292, GO-ESP)
T=0.0002 (1/6404, 1000G_30x)
T=0.0002 (1/5008, 1000G)
Clinical Significance
Reported in ClinVar
Gene : Consequence
NOTCH1 : Missense Variant
LOC124902310 : 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 91496 C=0.99995 T=0.00005
European Sub 68872 C=0.99997 T=0.00003
African Sub 8242 C=0.9998 T=0.0002
African Others Sub 298 C=1.000 T=0.000
African American Sub 7944 C=0.9997 T=0.0003
Asian Sub 3122 C=1.0000 T=0.0000
East Asian Sub 1908 C=1.0000 T=0.0000
Other Asian Sub 1214 C=1.0000 T=0.0000
Latin American 1 Sub 490 C=1.000 T=0.000
Latin American 2 Sub 644 C=1.000 T=0.000
South Asian Sub 104 C=1.000 T=0.000
Other Sub 10022 C=0.99990 T=0.00010


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=0.999841 T=0.000159
gnomAD - Exomes Global Study-wide 190032 C=0.999958 T=0.000042
gnomAD - Exomes European Sub 97916 C=0.99997 T=0.00003
gnomAD - Exomes Asian Sub 39568 C=1.00000 T=0.00000
gnomAD - Exomes American Sub 27414 C=0.99996 T=0.00004
gnomAD - Exomes African Sub 11362 C=0.99965 T=0.00035
gnomAD - Exomes Ashkenazi Jewish Sub 8888 C=1.0000 T=0.0000
gnomAD - Exomes Other Sub 4884 C=1.0000 T=0.0000
gnomAD - Genomes Global Study-wide 140292 C=0.999872 T=0.000128
gnomAD - Genomes European Sub 75962 C=0.99993 T=0.00007
gnomAD - Genomes African Sub 42052 C=0.99971 T=0.00029
gnomAD - Genomes American Sub 13670 C=0.99993 T=0.00007
gnomAD - Genomes Ashkenazi Jewish Sub 3324 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3132 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2152 C=1.0000 T=0.0000
Allele Frequency Aggregator Total Global 75762 C=0.99996 T=0.00004
Allele Frequency Aggregator European Sub 59264 C=0.99998 T=0.00002
Allele Frequency Aggregator Other Sub 8660 C=0.9999 T=0.0001
Allele Frequency Aggregator African Sub 3478 C=0.9997 T=0.0003
Allele Frequency Aggregator Asian Sub 3122 C=1.0000 T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 644 C=1.000 T=0.000
Allele Frequency Aggregator Latin American 1 Sub 490 C=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 104 C=1.000 T=0.000
14KJPN JAPANESE Study-wide 28258 C=0.99996 T=0.00004
ExAC Global Study-wide 27838 C=0.99986 T=0.00014
ExAC Europe Sub 13568 C=0.99993 T=0.00007
ExAC Asian Sub 10190 C=1.00000 T=0.00000
ExAC African Sub 3020 C=0.9990 T=0.0010
ExAC American Sub 836 C=1.000 T=0.000
ExAC Other Sub 224 C=1.000 T=0.000
GO Exome Sequencing Project Global Study-wide 12292 C=0.99959 T=0.00041
GO Exome Sequencing Project European American Sub 8300 C=0.9999 T=0.0001
GO Exome Sequencing Project African American Sub 3992 C=0.9990 T=0.0010
1000Genomes_30x Global Study-wide 6404 C=0.9998 T=0.0002
1000Genomes_30x African Sub 1786 C=1.0000 T=0.0000
1000Genomes_30x Europe Sub 1266 C=0.9992 T=0.0008
1000Genomes_30x South Asian Sub 1202 C=1.0000 T=0.0000
1000Genomes_30x East Asian Sub 1170 C=1.0000 T=0.0000
1000Genomes_30x American Sub 980 C=1.000 T=0.000
1000Genomes Global Study-wide 5008 C=0.9998 T=0.0002
1000Genomes African Sub 1322 C=1.0000 T=0.0000
1000Genomes East Asian Sub 1008 C=1.0000 T=0.0000
1000Genomes Europe Sub 1006 C=0.9990 T=0.0010
1000Genomes South Asian Sub 978 C=1.000 T=0.000
1000Genomes American Sub 694 C=1.000 T=0.000
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 9 NC_000009.12:g.136514511C>A
GRCh38.p14 chr 9 NC_000009.12:g.136514511C>G
GRCh38.p14 chr 9 NC_000009.12:g.136514511C>T
GRCh37.p13 chr 9 NC_000009.11:g.139408963C>A
GRCh37.p13 chr 9 NC_000009.11:g.139408963C>G
GRCh37.p13 chr 9 NC_000009.11:g.139408963C>T
NOTCH1 RefSeqGene (LRG_1122) NG_007458.1:g.36276G>T
NOTCH1 RefSeqGene (LRG_1122) NG_007458.1:g.36276G>C
NOTCH1 RefSeqGene (LRG_1122) NG_007458.1:g.36276G>A
Gene: NOTCH1, notch receptor 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
NOTCH1 transcript NM_017617.5:c.2206G>T G [GGG] > W [TGG] Coding Sequence Variant
neurogenic locus notch homolog protein 1 preproprotein NP_060087.3:p.Gly736Trp G (Gly) > W (Trp) Missense Variant
NOTCH1 transcript NM_017617.5:c.2206G>C G [GGG] > R [CGG] Coding Sequence Variant
neurogenic locus notch homolog protein 1 preproprotein NP_060087.3:p.Gly736Arg G (Gly) > R (Arg) Missense Variant
NOTCH1 transcript NM_017617.5:c.2206G>A G [GGG] > R [AGG] Coding Sequence Variant
neurogenic locus notch homolog protein 1 preproprotein NP_060087.3:p.Gly736Arg G (Gly) > R (Arg) Missense Variant
NOTCH1 transcript variant X1 XM_011518717.3:c.1483G>T G [GGG] > W [TGG] Coding Sequence Variant
neurogenic locus notch homolog protein 1 isoform X1 XP_011517019.2:p.Gly495Trp G (Gly) > W (Trp) Missense Variant
NOTCH1 transcript variant X1 XM_011518717.3:c.1483G>C G [GGG] > R [CGG] Coding Sequence Variant
neurogenic locus notch homolog protein 1 isoform X1 XP_011517019.2:p.Gly495Arg G (Gly) > R (Arg) Missense Variant
NOTCH1 transcript variant X1 XM_011518717.3:c.1483G>A G [GGG] > R [AGG] Coding Sequence Variant
neurogenic locus notch homolog protein 1 isoform X1 XP_011517019.2:p.Gly495Arg G (Gly) > R (Arg) Missense Variant
Gene: LOC124902310, uncharacterized LOC124902310 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC124902310 transcript variant X2 XR_007061865.1:n. N/A Intron Variant
LOC124902310 transcript variant X1 XR_007061864.1:n. 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.

Allele: T (allele ID: 425839 )
ClinVar Accession Disease Names Clinical Significance
RCV000498590.3 not provided Uncertain-Significance
RCV000660151.1 Connective tissue disorder Likely-Benign
RCV000770643.1 Familial thoracic aortic aneurysm and aortic dissection Uncertain-Significance
RCV001216676.3 Adams-Oliver syndrome 5 Uncertain-Significance
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 G T
GRCh38.p14 chr 9 NC_000009.12:g.136514511= NC_000009.12:g.136514511C>A NC_000009.12:g.136514511C>G NC_000009.12:g.136514511C>T
GRCh37.p13 chr 9 NC_000009.11:g.139408963= NC_000009.11:g.139408963C>A NC_000009.11:g.139408963C>G NC_000009.11:g.139408963C>T
NOTCH1 RefSeqGene (LRG_1122) NG_007458.1:g.36276= NG_007458.1:g.36276G>T NG_007458.1:g.36276G>C NG_007458.1:g.36276G>A
NOTCH1 transcript NM_017617.5:c.2206= NM_017617.5:c.2206G>T NM_017617.5:c.2206G>C NM_017617.5:c.2206G>A
NOTCH1 transcript NM_017617.4:c.2206= NM_017617.4:c.2206G>T NM_017617.4:c.2206G>C NM_017617.4:c.2206G>A
NOTCH1 transcript NM_017617.3:c.2206= NM_017617.3:c.2206G>T NM_017617.3:c.2206G>C NM_017617.3:c.2206G>A
NOTCH1 transcript variant X1 XM_011518717.3:c.1483= XM_011518717.3:c.1483G>T XM_011518717.3:c.1483G>C XM_011518717.3:c.1483G>A
NOTCH1 transcript variant X1 XM_011518717.2:c.1483= XM_011518717.2:c.1483G>T XM_011518717.2:c.1483G>C XM_011518717.2:c.1483G>A
NOTCH1 transcript variant X1 XM_011518717.1:c.1507= XM_011518717.1:c.1507G>T XM_011518717.1:c.1507G>C XM_011518717.1:c.1507G>A
neurogenic locus notch homolog protein 1 preproprotein NP_060087.3:p.Gly736= NP_060087.3:p.Gly736Trp NP_060087.3:p.Gly736Arg NP_060087.3:p.Gly736Arg
neurogenic locus notch homolog protein 1 isoform X1 XP_011517019.2:p.Gly495= XP_011517019.2:p.Gly495Trp XP_011517019.2:p.Gly495Arg XP_011517019.2:p.Gly495Arg
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#.

32 SubSNP, 9 Frequency, 4 ClinVar submissions
No Submitter Submission ID Date (Build)
1 EXOME_CHIP ss491430747 May 04, 2012 (137)
2 NHLBI-ESP ss712921153 Apr 25, 2013 (138)
3 ILLUMINA ss783568891 Sep 08, 2015 (146)
4 1000GENOMES ss1335853344 Aug 21, 2014 (142)
5 EVA_EXAC ss1689753775 Apr 01, 2015 (144)
6 ILLUMINA ss1752766348 Sep 08, 2015 (146)
7 ILLUMINA ss1917843171 Feb 12, 2016 (147)
8 ILLUMINA ss1946272762 Feb 12, 2016 (147)
9 ILLUMINA ss1959228586 Feb 12, 2016 (147)
10 HUMAN_LONGEVITY ss2315257293 Dec 20, 2016 (150)
11 GNOMAD ss2738018052 Nov 08, 2017 (151)
12 GNOMAD ss2748314980 Nov 08, 2017 (151)
13 GNOMAD ss2884332809 Nov 08, 2017 (151)
14 ILLUMINA ss3022978188 Nov 08, 2017 (151)
15 ILLUMINA ss3635239146 Oct 12, 2018 (152)
16 ILLUMINA ss3640946435 Oct 12, 2018 (152)
17 ILLUMINA ss3645006088 Oct 12, 2018 (152)
18 ILLUMINA ss3653535375 Oct 12, 2018 (152)
19 ILLUMINA ss3726654045 Jul 13, 2019 (153)
20 ILLUMINA ss3744596098 Jul 13, 2019 (153)
21 ILLUMINA ss3745539020 Jul 13, 2019 (153)
22 ILLUMINA ss3773030763 Jul 13, 2019 (153)
23 EVA ss3824487298 Apr 26, 2020 (154)
24 TOPMED ss4839026501 Apr 26, 2021 (155)
25 EVA ss5390910303 Oct 16, 2022 (156)
26 HUGCELL_USP ss5478365774 Oct 16, 2022 (156)
27 1000G_HIGH_COVERAGE ss5575760836 Oct 16, 2022 (156)
28 TOMMO_GENOMICS ss5740461809 Oct 16, 2022 (156)
29 EVA ss5848224534 Oct 16, 2022 (156)
30 EVA ss5918433801 Oct 16, 2022 (156)
31 EVA ss5936011656 Oct 16, 2022 (156)
32 EVA ss5977675141 Oct 16, 2022 (156)
33 1000Genomes NC_000009.11 - 139408963 Oct 12, 2018 (152)
34 1000Genomes_30x NC_000009.12 - 136514511 Oct 16, 2022 (156)
35 ExAC NC_000009.11 - 139408963 Oct 12, 2018 (152)
36 gnomAD - Genomes NC_000009.12 - 136514511 Apr 26, 2021 (155)
37 gnomAD - Exomes NC_000009.11 - 139408963 Jul 13, 2019 (153)
38 GO Exome Sequencing Project NC_000009.11 - 139408963 Oct 12, 2018 (152)
39 14KJPN NC_000009.12 - 136514511 Oct 16, 2022 (156)
40 TopMed NC_000009.12 - 136514511 Apr 26, 2021 (155)
41 ALFA NC_000009.12 - 136514511 Apr 26, 2021 (155)
42 ClinVar RCV000498590.3 Oct 16, 2022 (156)
43 ClinVar RCV000660151.1 Oct 12, 2018 (152)
44 ClinVar RCV000770643.1 Jul 13, 2019 (153)
45 ClinVar RCV001216676.3 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
ss5936011656 NC_000009.11:139408962:C:A NC_000009.12:136514510:C:A
ss5936011656 NC_000009.11:139408962:C:G NC_000009.12:136514510:C:G
48185237, 9896399, 7209282, 945031, ss491430747, ss712921153, ss783568891, ss1335853344, ss1689753775, ss1752766348, ss1917843171, ss1946272762, ss1959228586, ss2738018052, ss2748314980, ss2884332809, ss3022978188, ss3635239146, ss3640946435, ss3645006088, ss3653535375, ss3744596098, ss3745539020, ss3773030763, ss3824487298, ss5390910303, ss5848224534, ss5936011656, ss5977675141 NC_000009.11:139408962:C:T NC_000009.12:136514510:C:T (self)
RCV000498590.3, RCV000660151.1, RCV000770643.1, RCV001216676.3, 63286771, 340492178, 74298913, 676404062, 3820404321, ss2315257293, ss3726654045, ss4839026501, ss5478365774, ss5575760836, ss5740461809, ss5918433801 NC_000009.12:136514510:C:T NC_000009.12:136514510:C: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 rs201662530

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