Name: rs1799770
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.

rs1799770

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:156879118 (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: delA
Variation Type: Deletion
Frequency: delA=0.066886 (17704/264690, TOPMED)
delA=0.059322 (14732/248338, GnomAD_exome)
delA=0.063161 (8852/140150, GnomAD) (+ 14 more)
delA=0.062500 (7482/119712, ExAC)
delA=0.04562 (1289/28256, 14KJPN)
delA=0.03055 (799/26150, ALFA)
delA=0.04666 (782/16760, 8.3KJPN)
delA=0.06670 (835/12518, GO-ESP)
delA=0.0881 (564/6404, 1000G_30x)
delA=0.0893 (447/5008, 1000G)
delA=0.0306 (137/4480, Estonian)
delA=0.0475 (183/3854, ALSPAC)
delA=0.0504 (187/3708, TWINSUK)
delA=0.0660 (121/1832, Korea1K)
delA=0.043 (43/998, GoNL)
delA=0.035 (21/600, NorthernSweden)
delA=0.10 (4/40, GENOME_DK)

Clinical Significance: Reported in ClinVar
Gene : Consequence: NTRK1 : Intron 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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	Alt HMOZ	HTRZ	HWEP
Total	Global	26150	A=0.96945	=0.03055	0.940727	0.001836	0.057438	7
European	Sub	19536	A=0.97036	=0.02964	0.942465	0.00174	0.055794	5
African	Sub	2924	A=0.9819	=0.0181	0.964432	0.000684	0.034884	0
African Others	Sub	104	A=0.990	=0.010	0.980769	0.0	0.019231	0
African American	Sub	2820	A=0.9816	=0.0184	0.96383	0.000709	0.035461	0
Asian	Sub	162	A=0.963	=0.037	0.938272	0.012346	0.049383	5
East Asian	Sub	108	A=0.963	=0.037	0.944444	0.018519	0.037037	7
Other Asian	Sub	54	A=0.96	=0.04	0.925926	0.0	0.074074	0
Latin American 1	Sub	126	A=1.000	=0.000	1.0	0.0	0.0	N/A
Latin American 2	Sub	570	A=1.000	=0.000	1.0	0.0	0.0	N/A
South Asian	Sub	84	A=0.98	=0.02	0.952381	0.0	0.047619	0
Other	Sub	2748	A=0.9421	=0.0579	0.887918	0.003639	0.108443	0

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	A=0.933114	delA=0.066886
gnomAD - Exomes	Global	Study-wide	248338	A=0.940678	delA=0.059322
gnomAD - Exomes	European	Sub	132822	A=0.958697	delA=0.041303
gnomAD - Exomes	Asian	Sub	48986	A=0.88966	delA=0.11034
gnomAD - Exomes	American	Sub	34550	A=0.96813	delA=0.03187
gnomAD - Exomes	African	Sub	15830	A=0.88718	delA=0.11282
gnomAD - Exomes	Ashkenazi Jewish	Sub	10056	A=0.93954	delA=0.06046
gnomAD - Exomes	Other	Sub	6094	A=0.9432	delA=0.0568
gnomAD - Genomes	Global	Study-wide	140150	A=0.936839	delA=0.063161
gnomAD - Genomes	European	Sub	75922	A=0.95923	delA=0.04077
gnomAD - Genomes	African	Sub	41974	A=0.89563	delA=0.10437
gnomAD - Genomes	American	Sub	13652	A=0.94162	delA=0.05838
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	A=0.9377	delA=0.0623
gnomAD - Genomes	East Asian	Sub	3130	A=0.9252	delA=0.0748
gnomAD - Genomes	Other	Sub	2148	A=0.9358	delA=0.0642
ExAC	Global	Study-wide	119712	A=0.937500	delA=0.062500
ExAC	Europe	Sub	72458	A=0.95723	delA=0.04277
ExAC	Asian	Sub	25044	A=0.88644	delA=0.11356
ExAC	American	Sub	11532	A=0.96974	delA=0.03026
ExAC	African	Sub	9786	A=0.8845	delA=0.1155
ExAC	Other	Sub	892	A=0.933	delA=0.067
14KJPN	JAPANESE	Study-wide	28256	A=0.95438	delA=0.04562
Allele Frequency Aggregator	Total	Global	26150	A=0.96945	delA=0.03055
Allele Frequency Aggregator	European	Sub	19536	A=0.97036	delA=0.02964
Allele Frequency Aggregator	African	Sub	2924	A=0.9819	delA=0.0181
Allele Frequency Aggregator	Other	Sub	2748	A=0.9421	delA=0.0579
Allele Frequency Aggregator	Latin American 2	Sub	570	A=1.000	delA=0.000
Allele Frequency Aggregator	Asian	Sub	162	A=0.963	delA=0.037
Allele Frequency Aggregator	Latin American 1	Sub	126	A=1.000	delA=0.000
Allele Frequency Aggregator	South Asian	Sub	84	A=0.98	delA=0.02
8.3KJPN	JAPANESE	Study-wide	16760	A=0.95334	delA=0.04666
GO Exome Sequencing Project	Global	Study-wide	12518	A=0.93330	delA=0.06670
GO Exome Sequencing Project	European American	Sub	8252	A=0.9527	delA=0.0473
GO Exome Sequencing Project	African American	Sub	4266	A=0.8957	delA=0.1043
1000Genomes_30x	Global	Study-wide	6404	A=0.9119	delA=0.0881
1000Genomes_30x	African	Sub	1786	A=0.8718	delA=0.1282
1000Genomes_30x	Europe	Sub	1266	A=0.9573	delA=0.0427
1000Genomes_30x	South Asian	Sub	1202	A=0.8902	delA=0.1098
1000Genomes_30x	East Asian	Sub	1170	A=0.9111	delA=0.0889
1000Genomes_30x	American	Sub	980	A=0.954	delA=0.046
1000Genomes	Global	Study-wide	5008	A=0.9107	delA=0.0893
1000Genomes	African	Sub	1322	A=0.8691	delA=0.1309
1000Genomes	East Asian	Sub	1008	A=0.9137	delA=0.0863
1000Genomes	Europe	Sub	1006	A=0.9513	delA=0.0487
1000Genomes	South Asian	Sub	978	A=0.890	delA=0.110
1000Genomes	American	Sub	694	A=0.957	delA=0.043
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.9694	delA=0.0306
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.9525	delA=0.0475
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.9496	delA=0.0504
Korean Genome Project	KOREAN	Study-wide	1832	A=0.9340	delA=0.0660
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.957	delA=0.043
Northern Sweden	ACPOP	Study-wide	600	A=0.965	delA=0.035
The Danish reference pan genome	Danish	Study-wide	40	A=0.90	delA=0.10

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 1	NC_000001.11:g.156879118del
GRCh37.p13 chr 1	NC_000001.10:g.156848910del
NTRK1 RefSeqGene (LRG_261)	NG_007493.1:g.68369del

Gene: NTRK1, neurotrophic receptor tyrosine kinase 1 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
NTRK1 transcript variant 3	NM_001007792.1:c.1698-4del	N/A	Intron Variant
NTRK1 transcript variant 1	NM_001012331.2:c.1788-4del	N/A	Intron Variant
NTRK1 transcript variant 2	NM_002529.4:c.1806-4del	N/A	Intron 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: delA (allele ID: 277584 )

ClinVar Accession	Disease Names	Clinical Significance
RCV000328341.15	Hereditary insensitivity to pain with anhidrosis	Benign-Likely-Benign
RCV000712457.3	not provided	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	A=	delA
GRCh38.p14 chr 1	NC_000001.11:g.156879118=	NC_000001.11:g.156879118del
GRCh37.p13 chr 1	NC_000001.10:g.156848910=	NC_000001.10:g.156848910del
NTRK1 RefSeqGene (LRG_261)	NG_007493.1:g.68369=	NG_007493.1:g.68369del
NTRK1 transcript variant 3	NM_001007792.1:c.1698-4=	NM_001007792.1:c.1698-4del
NTRK1 transcript variant 1	NM_001012331.1:c.1788-4=	NM_001012331.1:c.1788-4del
NTRK1 transcript variant 1	NM_001012331.2:c.1788-4=	NM_001012331.2:c.1788-4del
NTRK1 transcript variant 2	NM_002529.3:c.1806-4=	NM_002529.3:c.1806-4del
NTRK1 transcript variant 2	NM_002529.4:c.1806-4=	NM_002529.4:c.1806-4del
NTRK1 transcript variant X1	XM_005245219.1:c.1875-4=	XM_005245219.1:c.1875-4del

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#.

55 SubSNP, 17 Frequency, 2 ClinVar submissions

No	Submitter	Submission ID	Date (Build)
1	HGBASE	ss2419780	Nov 14, 2000 (89)
2	YUSUKE	ss5018407	Aug 28, 2002 (110)
3	DEVINE_LAB	ss102411374	Mar 15, 2016 (147)
4	BUSHMAN	ss193130239	Jul 04, 2010 (132)
5	PJP	ss294605521	May 09, 2011 (134)
6	1000GENOMES	ss326087991	May 09, 2011 (137)
7	1000GENOMES	ss326091098	May 09, 2011 (137)
8	1000GENOMES	ss326119901	May 09, 2011 (137)
9	1000GENOMES	ss499004691	May 04, 2012 (137)
10	LUNTER	ss550983191	Apr 25, 2013 (138)
11	LUNTER	ss551000621	Apr 25, 2013 (138)
12	LUNTER	ss552808614	Apr 25, 2013 (138)
13	TISHKOFF	ss553780145	Apr 25, 2013 (138)
14	SSMP	ss663123428	Apr 01, 2015 (144)
15	EVA-GONL	ss975696377	Aug 21, 2014 (142)
16	1000GENOMES	ss1367862026	Aug 21, 2014 (142)
17	EVA_GENOME_DK	ss1574031051	Apr 01, 2015 (144)
18	EVA_DECODE	ss1585078563	Apr 01, 2015 (144)
19	EVA_UK10K_ALSPAC	ss1701273421	Apr 01, 2015 (144)
20	EVA_UK10K_TWINSUK	ss1701273505	Apr 01, 2015 (144)
21	EVA_EXAC	ss1711640616	Apr 01, 2015 (144)
22	HAMMER_LAB	ss1795108319	Sep 08, 2015 (146)
23	JJLAB	ss2030350479	Sep 14, 2016 (149)
24	SYSTEMSBIOZJU	ss2624497821	Nov 08, 2017 (151)
25	GNOMAD	ss2731950633	Nov 08, 2017 (151)
26	GNOMAD	ss2746467044	Nov 08, 2017 (151)
27	GNOMAD	ss2761496300	Nov 08, 2017 (151)
28	AFFY	ss2984880658	Nov 08, 2017 (151)
29	AFFY	ss2985525702	Nov 08, 2017 (151)
30	SWEGEN	ss2987776569	Nov 08, 2017 (151)
31	MCHAISSO	ss3065329499	Nov 08, 2017 (151)
32	ILLUMINA	ss3653649904	Oct 11, 2018 (152)
33	EGCUT_WGS	ss3655715720	Jul 12, 2019 (153)
34	EVA_DECODE	ss3687812159	Jul 12, 2019 (153)
35	ACPOP	ss3727496660	Jul 12, 2019 (153)
36	KHV_HUMAN_GENOMES	ss3799824453	Jul 12, 2019 (153)
37	EVA	ss3823670372	Apr 25, 2020 (154)
38	KOGIC	ss3945686223	Apr 25, 2020 (154)
39	EVA	ss3986141306	Apr 25, 2021 (155)
40	TOPMED	ss4468853281	Apr 25, 2021 (155)
41	TOMMO_GENOMICS	ss5146558889	Apr 25, 2021 (155)
42	EVA	ss5237633029	Oct 12, 2022 (156)
43	1000G_HIGH_COVERAGE	ss5244344630	Oct 12, 2022 (156)
44	TRAN_CS_UWATERLOO	ss5314397609	Oct 12, 2022 (156)
45	HUGCELL_USP	ss5444931661	Oct 12, 2022 (156)
46	1000G_HIGH_COVERAGE	ss5517698694	Oct 12, 2022 (156)
47	EVA	ss5623890667	Oct 12, 2022 (156)
48	EVA	ss5623998302	Oct 12, 2022 (156)
49	SANFORD_IMAGENETICS	ss5626618491	Oct 12, 2022 (156)
50	TOMMO_GENOMICS	ss5673781023	Oct 12, 2022 (156)
51	YY_MCH	ss5801271688	Oct 12, 2022 (156)
52	EVA	ss5832684492	Oct 12, 2022 (156)
53	EVA	ss5848274199	Oct 12, 2022 (156)
54	EVA	ss5910303144	Oct 12, 2022 (156)
55	EVA	ss5938413106	Oct 12, 2022 (156)
56	1000Genomes	NC_000001.10 - 156848910	Oct 11, 2018 (152)
57	1000Genomes_30x	NC_000001.11 - 156879118	Oct 12, 2022 (156)
58	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 156848910	Oct 11, 2018 (152)
59	Genetic variation in the Estonian population	NC_000001.10 - 156848910	Oct 11, 2018 (152)
60	ExAC	NC_000001.10 - 156848910	Oct 11, 2018 (152)
61	The Danish reference pan genome	NC_000001.10 - 156848910	Apr 25, 2020 (154)
62	gnomAD - Genomes	NC_000001.11 - 156879118	Apr 25, 2021 (155)
63	gnomAD - Exomes	NC_000001.10 - 156848910	Jul 12, 2019 (153)
64	GO Exome Sequencing Project	NC_000001.10 - 156848910	Oct 11, 2018 (152)
65	Genome of the Netherlands Release 5	NC_000001.10 - 156848910	Apr 25, 2020 (154)
66	Korean Genome Project	NC_000001.11 - 156879118	Apr 25, 2020 (154)
67	Northern Sweden	NC_000001.10 - 156848910	Jul 12, 2019 (153)
68	8.3KJPN	NC_000001.10 - 156848910	Apr 25, 2021 (155)
69	14KJPN	NC_000001.11 - 156879118	Oct 12, 2022 (156)
70	TopMed	NC_000001.11 - 156879118	Apr 25, 2021 (155)
71	UK 10K study - Twins	NC_000001.10 - 156848910	Oct 11, 2018 (152)
72	ALFA	NC_000001.11 - 156879118	Apr 25, 2021 (155)
73	ClinVar	RCV000328341.15	Oct 12, 2022 (156)
74	ClinVar	RCV000712457.3	Oct 12, 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).

Associated ID	History Updated (Build)
rs3831902	Dec 16, 2002 (110)
rs141073644	May 04, 2012 (137)
rs374982600	May 13, 2013 (138)
rs869214279	Jul 19, 2016 (147)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss294605521, ss326087991, ss326091098, ss326119901, ss550983191, ss551000621, ss552808614, ss1585078563	NC_000001.9:155115533:A:	NC_000001.11:156879117:A:	(self)
3778075, 2053936, 1453968, 5063787, 174350, 974502, 128954, 891017, 781525, 4528196, 2053936, ss499004691, ss553780145, ss663123428, ss975696377, ss1367862026, ss1574031051, ss1701273421, ss1701273505, ss1711640616, ss1795108319, ss2030350479, ss2624497821, ss2731950633, ss2746467044, ss2761496300, ss2984880658, ss2985525702, ss2987776569, ss3653649904, ss3655715720, ss3727496660, ss3823670372, ss3986141306, ss5146558889, ss5623890667, ss5623998302, ss5626618491, ss5832684492, ss5848274199, ss5938413106	NC_000001.10:156848909:A:	NC_000001.11:156879117:A:	(self)
RCV000328341.15, RCV000712457.3, 5224629, 27515174, 2064224, 7618127, 32459616, 7986417383, ss3065329499, ss3687812159, ss3799824453, ss3945686223, ss4468853281, ss5237633029, ss5244344630, ss5314397609, ss5444931661, ss5517698694, ss5673781023, ss5801271688, ss5910303144	NC_000001.11:156879117:A:	NC_000001.11:156879117:A:	(self)
ss2419780, ss5018407, ss102411374	NT_004487.19:8337551:A:	NC_000001.11:156879117:A:	(self)
ss193130239	NT_004487.20:13694530:A:	NC_000001.11:156879117:A:	(self)

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

1 citation for rs1799770

PMID	Title	Author	Year	Journal
17212826	TAMGeS: a Three-array Method for Genotyping of SNPs by a dual-colour approach.	Cozza A et al.	2007	BMC genomics

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs1799770