Name: rs61751489
Published: September 21, 2022
License: Open Access

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.

rs61751489

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr9:136496886 (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>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.026012 (6885/264690, TOPMED)
T=0.031181 (7684/246434, GnomAD_exome)
T=0.018494 (2594/140262, GnomAD) (+ 17 more)
T=0.025411 (2952/116172, ExAC)
T=0.016783 (1929/114936, ALFA)
T=0.01245 (155/12446, GO-ESP)
T=0.0239 (153/6404, 1000G_30x)
T=0.0212 (106/5008, 1000G)
T=0.0085 (38/4480, Estonian)
T=0.0215 (83/3854, ALSPAC)
T=0.0165 (61/3708, TWINSUK)
T=0.003 (2/600, NorthernSweden)
T=0.017 (9/534, MGP)
T=0.010 (3/302, FINRISK)
T=0.005 (1/216, Qatari)
T=0.03 (1/40, GENOME_DK)
C=0.50 (15/30, SGDP_PRJ)
T=0.50 (15/30, SGDP_PRJ)
C=0.5 (2/4, Siberian)
T=0.5 (2/4, Siberian)

Clinical Significance: Reported in ClinVar
Gene : Consequence: NOTCH1 : Missense Variant
Publications: 2 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	131342	C=0.983669	T=0.016331
European	Sub	107360	C=0.984026	T=0.015974
African	Sub	8540	C=0.9944	T=0.0056
African Others	Sub	308	C=1.000	T=0.000
African American	Sub	8232	C=0.9942	T=0.0058
Asian	Sub	216	C=0.958	T=0.042
East Asian	Sub	134	C=0.933	T=0.067
Other Asian	Sub	82	C=1.00	T=0.00
Latin American 1	Sub	500	C=0.964	T=0.036
Latin American 2	Sub	648	C=0.860	T=0.140
South Asian	Sub	98	C=1.00	T=0.00
Other	Sub	13980	C=0.98112	T=0.01888

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").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	C=0.973988	T=0.026012
gnomAD - Exomes	Global	Study-wide	246434	C=0.968819	T=0.031181
gnomAD - Exomes	European	Sub	132540	C=0.986034	T=0.013966
gnomAD - Exomes	Asian	Sub	48518	C=0.99648	T=0.00352
gnomAD - Exomes	American	Sub	34446	C=0.84315	T=0.15685
gnomAD - Exomes	African	Sub	14996	C=0.99487	T=0.00513
gnomAD - Exomes	Ashkenazi Jewish	Sub	9934	C=0.9957	T=0.0043
gnomAD - Exomes	Other	Sub	6000	C=0.9768	T=0.0232
gnomAD - Genomes	Global	Study-wide	140262	C=0.981506	T=0.018494
gnomAD - Genomes	European	Sub	75950	C=0.98627	T=0.01373
gnomAD - Genomes	African	Sub	42044	C=0.99460	T=0.00540
gnomAD - Genomes	American	Sub	13664	C=0.90837	T=0.09163
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	C=0.9952	T=0.0048
gnomAD - Genomes	East Asian	Sub	3132	C=0.9997	T=0.0003
gnomAD - Genomes	Other	Sub	2152	C=0.9744	T=0.0256
ExAC	Global	Study-wide	116172	C=0.974589	T=0.025411
ExAC	Europe	Sub	69900	C=0.98628	T=0.01372
ExAC	Asian	Sub	24994	C=0.99608	T=0.00392
ExAC	American	Sub	11432	C=0.83992	T=0.16008
ExAC	African	Sub	8982	C=0.9944	T=0.0056
ExAC	Other	Sub	864	C=0.983	T=0.017
Allele Frequency Aggregator	Total	Global	114936	C=0.983217	T=0.016783
Allele Frequency Aggregator	European	Sub	97226	C=0.98402	T=0.01598
Allele Frequency Aggregator	Other	Sub	12546	C=0.98135	T=0.01865
Allele Frequency Aggregator	African	Sub	3702	C=0.9938	T=0.0062
Allele Frequency Aggregator	Latin American 2	Sub	648	C=0.860	T=0.140
Allele Frequency Aggregator	Latin American 1	Sub	500	C=0.964	T=0.036
Allele Frequency Aggregator	Asian	Sub	216	C=0.958	T=0.042
Allele Frequency Aggregator	South Asian	Sub	98	C=1.00	T=0.00
GO Exome Sequencing Project	Global	Study-wide	12446	C=0.98755	T=0.01245
GO Exome Sequencing Project	European American	Sub	8352	C=0.9838	T=0.0162
GO Exome Sequencing Project	African American	Sub	4094	C=0.9951	T=0.0049
1000Genomes_30x	Global	Study-wide	6404	C=0.9761	T=0.0239
1000Genomes_30x	African	Sub	1786	C=0.9994	T=0.0006
1000Genomes_30x	Europe	Sub	1266	C=0.9826	T=0.0174
1000Genomes_30x	South Asian	Sub	1202	C=0.9967	T=0.0033
1000Genomes_30x	East Asian	Sub	1170	C=1.0000	T=0.0000
1000Genomes_30x	American	Sub	980	C=0.871	T=0.129
1000Genomes	Global	Study-wide	5008	C=0.9788	T=0.0212
1000Genomes	African	Sub	1322	C=0.9992	T=0.0008
1000Genomes	East Asian	Sub	1008	C=1.0000	T=0.0000
1000Genomes	Europe	Sub	1006	C=0.9831	T=0.0169
1000Genomes	South Asian	Sub	978	C=0.997	T=0.003
1000Genomes	American	Sub	694	C=0.878	T=0.122
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.9915	T=0.0085
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.9785	T=0.0215
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.9835	T=0.0165
Northern Sweden	ACPOP	Study-wide	600	C=0.997	T=0.003
Medical Genome Project healthy controls from Spanish population	Spanish controls	Study-wide	534	C=0.983	T=0.017
FINRISK	Finnish from FINRISK project	Study-wide	302	C=0.990	T=0.010
Qatari	Global	Study-wide	216	C=0.995	T=0.005
The Danish reference pan genome	Danish	Study-wide	40	C=0.97	T=0.03
SGDP_PRJ	Global	Study-wide	30	C=0.50	T=0.50
Siberian	Global	Study-wide	4	C=0.5	T=0.5

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.136496886C>T
GRCh37.p13 chr 9	NC_000009.11:g.139391338C>T
NOTCH1 RefSeqGene (LRG_1122)	NG_007458.1:g.53901G>A

Gene: NOTCH1, notch receptor 1 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
NOTCH1 transcript	NM_017617.5:c.6853G>A	V [GTC] > I [ATC]	Coding Sequence Variant
neurogenic locus notch homolog protein 1 preproprotein	NP_060087.3:p.Val2285Ile	V (Val) > I (Ile)	Missense Variant
NOTCH1 transcript variant X1	XM_011518717.3:c.6130G>A	V [GTC] > I [ATC]	Coding Sequence Variant
neurogenic locus notch homolog protein 1 isoform X1	XP_011517019.2:p.Val2044I… XP_011517019.2:p.Val2044Ile	V (Val) > I (Ile)	Missense Variant

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: 138693 )

ClinVar Accession	Disease Names	Clinical Significance
RCV000121704.9	not specified	Benign
RCV000463376.8	Adams-Oliver syndrome 5	Benign
RCV000618803.1	Cardiovascular phenotype	Benign
RCV001291517.1	Hypoplastic left heart syndrome	Uncertain-Significance
RCV001573999.1	not provided	Likely-Benign
RCV002269866.1	Aortic valve disease 1	Benign

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=	T
GRCh38.p14 chr 9	NC_000009.12:g.136496886=	NC_000009.12:g.136496886C>T
GRCh37.p13 chr 9	NC_000009.11:g.139391338=	NC_000009.11:g.139391338C>T
NOTCH1 RefSeqGene (LRG_1122)	NG_007458.1:g.53901=	NG_007458.1:g.53901G>A
NOTCH1 transcript	NM_017617.5:c.6853=	NM_017617.5:c.6853G>A
NOTCH1 transcript	NM_017617.4:c.6853=	NM_017617.4:c.6853G>A
NOTCH1 transcript	NM_017617.3:c.6853=	NM_017617.3:c.6853G>A
NOTCH1 transcript variant X1	XM_011518717.3:c.6130=	XM_011518717.3:c.6130G>A
NOTCH1 transcript variant X1	XM_011518717.2:c.6130=	XM_011518717.2:c.6130G>A
NOTCH1 transcript variant X1	XM_011518717.1:c.6154=	XM_011518717.1:c.6154G>A
neurogenic locus notch homolog protein 1 preproprotein	NP_060087.3:p.Val2285=	NP_060087.3:p.Val2285Ile
neurogenic locus notch homolog protein 1 isoform X1	XP_011517019.2:p.Val2044=	XP_011517019.2:p.Val2044Ile

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#.

66 SubSNP, 18 Frequency, 6 ClinVar submissions

No	Submitter	Submission ID	Date (Build)
1	CANCER-GENOME	ss86344311	Mar 23, 2008 (129)
2	BCM-HGSC-SUB	ss206917515	Jul 04, 2010 (132)
3	1000GENOMES	ss335872662	May 09, 2011 (134)
4	1000GENOMES	ss490989863	May 04, 2012 (137)
5	EXOME_CHIP	ss491430715	May 04, 2012 (137)
6	CLINSEQ_SNP	ss491946732	May 04, 2012 (137)
7	ILLUMINA	ss535098810	Sep 08, 2015 (146)
8	NHLBI-ESP	ss712920815	Apr 25, 2013 (138)
9	ILLUMINA	ss783568858	Sep 08, 2015 (146)
10	EVA-GONL	ss987083158	Aug 21, 2014 (142)
11	JMKIDD_LAB	ss1067509480	Aug 21, 2014 (142)
12	JMKIDD_LAB	ss1076680009	Aug 21, 2014 (142)
13	1000GENOMES	ss1335852574	Aug 21, 2014 (142)
14	CLINVAR	ss1457610455	Nov 23, 2014 (142)
15	EVA_GENOME_DK	ss1583296780	Apr 01, 2015 (144)
16	EVA_FINRISK	ss1584065946	Apr 01, 2015 (144)
17	EVA_DECODE	ss1596730600	Apr 01, 2015 (144)
18	EVA_UK10K_ALSPAC	ss1623771692	Apr 01, 2015 (144)
19	EVA_UK10K_TWINSUK	ss1666765725	Apr 01, 2015 (144)
20	EVA_EXAC	ss1689752124	Apr 01, 2015 (144)
21	EVA_MGP	ss1711243489	Apr 01, 2015 (144)
22	ILLUMINA	ss1752766314	Sep 08, 2015 (146)
23	ILLUMINA	ss1917843145	Feb 12, 2016 (147)
24	WEILL_CORNELL_DGM	ss1930399454	Feb 12, 2016 (147)
25	ILLUMINA	ss1946272734	Feb 12, 2016 (147)
26	ILLUMINA	ss1959228510	Feb 12, 2016 (147)
27	JJLAB	ss2025922885	Sep 14, 2016 (149)
28	USC_VALOUEV	ss2154160640	Dec 20, 2016 (150)
29	HUMAN_LONGEVITY	ss2315255731	Dec 20, 2016 (150)
30	ILLUMINA	ss2711175798	Nov 08, 2017 (151)
31	GNOMAD	ss2738015764	Nov 08, 2017 (151)
32	GNOMAD	ss2748314192	Nov 08, 2017 (151)
33	GNOMAD	ss2884330825	Nov 08, 2017 (151)
34	SWEGEN	ss3005755914	Nov 08, 2017 (151)
35	CSHL	ss3348904088	Nov 08, 2017 (151)
36	ILLUMINA	ss3630381804	Oct 12, 2018 (152)
37	ILLUMINA	ss3635239111	Oct 12, 2018 (152)
38	ILLUMINA	ss3640946400	Oct 12, 2018 (152)
39	ILLUMINA	ss3645006061	Oct 12, 2018 (152)
40	OMUKHERJEE_ADBS	ss3646400509	Oct 12, 2018 (152)
41	EGCUT_WGS	ss3673292929	Jul 13, 2019 (153)
42	EVA_DECODE	ss3724959209	Jul 13, 2019 (153)
43	ACPOP	ss3736962576	Jul 13, 2019 (153)
44	ILLUMINA	ss3744596072	Jul 13, 2019 (153)
45	ILLUMINA	ss3745538985	Jul 13, 2019 (153)
46	EVA	ss3769816500	Jul 13, 2019 (153)
47	ILLUMINA	ss3773030729	Jul 13, 2019 (153)
48	KHV_HUMAN_GENOMES	ss3812976397	Jul 13, 2019 (153)
49	EVA	ss3824486951	Apr 26, 2020 (154)
50	EVA	ss3825767978	Apr 26, 2020 (154)
51	EVA	ss3831910677	Apr 26, 2020 (154)
52	SGDP_PRJ	ss3873287898	Apr 26, 2020 (154)
53	EVA	ss3986470258	Apr 26, 2021 (155)
54	TOPMED	ss4839020718	Apr 26, 2021 (155)
55	EVA	ss5237654249	Oct 16, 2022 (156)
56	1000G_HIGH_COVERAGE	ss5282539015	Oct 16, 2022 (156)
57	EVA	ss5390909079	Oct 16, 2022 (156)
58	HUGCELL_USP	ss5478365221	Oct 16, 2022 (156)
59	1000G_HIGH_COVERAGE	ss5575759892	Oct 16, 2022 (156)
60	EVA	ss5623892596	Oct 16, 2022 (156)
61	SANFORD_IMAGENETICS	ss5648460017	Oct 16, 2022 (156)
62	EVA	ss5829889546	Oct 16, 2022 (156)
63	EVA	ss5848224494	Oct 16, 2022 (156)
64	EVA	ss5848736027	Oct 16, 2022 (156)
65	EVA	ss5918433036	Oct 16, 2022 (156)
66	EVA	ss5977674801	Oct 16, 2022 (156)
67	1000Genomes	NC_000009.11 - 139391338	Oct 12, 2018 (152)
68	1000Genomes_30x	NC_000009.12 - 136496886	Oct 16, 2022 (156)
69	The Avon Longitudinal Study of Parents and Children	NC_000009.11 - 139391338	Oct 12, 2018 (152)
70	Genetic variation in the Estonian population	NC_000009.11 - 139391338	Oct 12, 2018 (152)
71	ExAC	NC_000009.11 - 139391338	Oct 12, 2018 (152)
72	FINRISK	NC_000009.11 - 139391338	Apr 26, 2020 (154)
73	The Danish reference pan genome	NC_000009.11 - 139391338	Apr 26, 2020 (154)
74	gnomAD - Genomes	NC_000009.12 - 136496886	Apr 26, 2021 (155)
75	gnomAD - Exomes	NC_000009.11 - 139391338	Jul 13, 2019 (153)
76	GO Exome Sequencing Project	NC_000009.11 - 139391338	Oct 12, 2018 (152)
77	Medical Genome Project healthy controls from Spanish population	NC_000009.11 - 139391338	Apr 26, 2020 (154)
78	Northern Sweden	NC_000009.11 - 139391338	Jul 13, 2019 (153)
79	Qatari	NC_000009.11 - 139391338	Apr 26, 2020 (154)
80	SGDP_PRJ	NC_000009.11 - 139391338	Apr 26, 2020 (154)
81	Siberian	NC_000009.11 - 139391338	Apr 26, 2020 (154)
82	TopMed	NC_000009.12 - 136496886	Apr 26, 2021 (155)
83	UK 10K study - Twins	NC_000009.11 - 139391338	Oct 12, 2018 (152)
84	ALFA	NC_000009.12 - 136496886	Apr 26, 2021 (155)
85	ClinVar	RCV000121704.9	Oct 16, 2022 (156)
86	ClinVar	RCV000463376.8	Oct 16, 2022 (156)
87	ClinVar	RCV000618803.1	Oct 12, 2018 (152)
88	ClinVar	RCV001291517.1	Apr 26, 2021 (155)
89	ClinVar	RCV001573999.1	Oct 16, 2022 (156)
90	ClinVar	RCV002269866.1	Oct 16, 2022 (156)

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
ss206917515, ss491946732, ss1596730600	NC_000009.10:138511158:C:T	NC_000009.12:136496885:C:T	(self)
48184451, 26778088, 19031177, 9894695, 62407, 9461717, 7206931, 944684, 359249, 10247441, 12441384, 25304878, 6676994, 26778088, ss335872662, ss490989863, ss491430715, ss535098810, ss712920815, ss783568858, ss987083158, ss1067509480, ss1076680009, ss1335852574, ss1583296780, ss1584065946, ss1623771692, ss1666765725, ss1689752124, ss1711243489, ss1752766314, ss1917843145, ss1930399454, ss1946272734, ss1959228510, ss2025922885, ss2154160640, ss2711175798, ss2738015764, ss2748314192, ss2884330825, ss3005755914, ss3348904088, ss3630381804, ss3635239111, ss3640946400, ss3645006061, ss3646400509, ss3673292929, ss3736962576, ss3744596072, ss3745538985, ss3769816500, ss3773030729, ss3824486951, ss3825767978, ss3831910677, ss3873287898, ss3986470258, ss5390909079, ss5623892596, ss5648460017, ss5829889546, ss5848224494, ss5848736027, ss5977674801	NC_000009.11:139391337:C:T	NC_000009.12:136496885:C:T	(self)
RCV000121704.9, RCV000463376.8, RCV000618803.1, RCV001291517.1, RCV001573999.1, RCV002269866.1, 63285827, 340487556, 676398279, 2567912749, ss1457610455, ss2315255731, ss3724959209, ss3812976397, ss4839020718, ss5237654249, ss5282539015, ss5478365221, ss5575759892, ss5918433036	NC_000009.12:136496885:C:T	NC_000009.12:136496885:C:T	(self)
ss86344311	NT_024000.16:174340:C:T	NC_000009.12:136496885:C:T	(self)

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

2 citations for rs61751489

PMID	Title	Author	Year	Journal
24728327	Germline variation in cancer-susceptibility genes in a healthy, ancestrally diverse cohort: implications for individual genome sequencing.	Bodian DL et al.	2014	PloS one
26708639	Identification of Gender-Specific Genetic Variants in Patients With Bicuspid Aortic Valve.	Dargis N et al.	2016	The American journal of cardiology

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs61751489