Name: rs111419170
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.

rs111419170

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:99115364 (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: A>C / A>G / A>T
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.120042 (31774/264690, TOPMED)
G=0.108275 (15162/140032, GnomAD)
A=0.28342 (8009/28258, 14KJPN) (+ 12 more)
G=0.11663 (2160/18520, ALFA)
A=0.27494 (4608/16760, 8.3KJPN)
G=0.2291 (1467/6404, 1000G_30x)
G=0.2482 (1243/5008, 1000G)
G=0.1136 (509/4480, Estonian)
A=0.3109 (911/2930, KOREAN)
A=0.3035 (556/1832, Korea1K)
G=0.127 (127/998, GoNL)
G=0.088 (53/600, NorthernSweden)
G=0.134 (29/216, Qatari)
A=0.370 (77/208, SGDP_PRJ)
G=0.12 (5/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LOC100507053 : 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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	Alt HMOZ	HTRZ	HWEP
Total	Global	18520	A=0.88337	G=0.11663	0.783693	0.016955	0.199352	6
European	Sub	14152	A=0.87429	G=0.12571	0.763426	0.014839	0.221735	0
African	Sub	2898	A=0.9669	G=0.0331	0.934438	0.00069	0.064872	0
African Others	Sub	114	A=0.982	G=0.018	0.964912	0.0	0.035088	0
African American	Sub	2784	A=0.9662	G=0.0338	0.93319	0.000718	0.066092	0
Asian	Sub	112	A=0.223	G=0.777	0.035714	0.589286	0.375	0
East Asian	Sub	86	A=0.23	G=0.77	0.023256	0.55814	0.418605	1
Other Asian	Sub	26	A=0.19	G=0.81	0.076923	0.692308	0.230769	1
Latin American 1	Sub	146	A=0.870	G=0.130	0.767123	0.027397	0.205479	0
Latin American 2	Sub	610	A=0.889	G=0.111	0.786885	0.009836	0.203279	0
South Asian	Sub	98	A=0.67	G=0.33	0.428571	0.081633	0.489796	0
Other	Sub	504	A=0.843	G=0.157	0.722222	0.035714	0.242063	1

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=0.879958	G=0.120042
gnomAD - Genomes	Global	Study-wide	140032	A=0.891725	G=0.108275
gnomAD - Genomes	European	Sub	75848	A=0.87876	G=0.12124
gnomAD - Genomes	African	Sub	42000	A=0.96743	G=0.03257
gnomAD - Genomes	American	Sub	13652	A=0.89386	G=0.10614
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	A=0.8238	G=0.1762
gnomAD - Genomes	East Asian	Sub	3066	A=0.2642	G=0.7358
gnomAD - Genomes	Other	Sub	2146	A=0.8565	G=0.1435
14KJPN	JAPANESE	Study-wide	28258	A=0.28342	G=0.71658
Allele Frequency Aggregator	Total	Global	18520	A=0.88337	G=0.11663
Allele Frequency Aggregator	European	Sub	14152	A=0.87429	G=0.12571
Allele Frequency Aggregator	African	Sub	2898	A=0.9669	G=0.0331
Allele Frequency Aggregator	Latin American 2	Sub	610	A=0.889	G=0.111
Allele Frequency Aggregator	Other	Sub	504	A=0.843	G=0.157
Allele Frequency Aggregator	Latin American 1	Sub	146	A=0.870	G=0.130
Allele Frequency Aggregator	Asian	Sub	112	A=0.223	G=0.777
Allele Frequency Aggregator	South Asian	Sub	98	A=0.67	G=0.33
8.3KJPN	JAPANESE	Study-wide	16760	A=0.27494	G=0.72506
1000Genomes_30x	Global	Study-wide	6404	A=0.7709	G=0.2291
1000Genomes_30x	African	Sub	1786	A=0.9866	G=0.0134
1000Genomes_30x	Europe	Sub	1266	A=0.8736	G=0.1264
1000Genomes_30x	South Asian	Sub	1202	A=0.6997	G=0.3003
1000Genomes_30x	East Asian	Sub	1170	A=0.2786	G=0.7214
1000Genomes_30x	American	Sub	980	A=0.920	G=0.080
1000Genomes	Global	Study-wide	5008	A=0.7518	G=0.2482
1000Genomes	African	Sub	1322	A=0.9849	G=0.0151
1000Genomes	East Asian	Sub	1008	A=0.2718	G=0.7282
1000Genomes	Europe	Sub	1006	A=0.8708	G=0.1292
1000Genomes	South Asian	Sub	978	A=0.694	G=0.306
1000Genomes	American	Sub	694	A=0.914	G=0.086
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.8864	G=0.1136
KOREAN population from KRGDB	KOREAN	Study-wide	2930	A=0.3109	C=0.0000, G=0.6891, T=0.0000
Korean Genome Project	KOREAN	Study-wide	1832	A=0.3035	G=0.6965
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.873	G=0.127
Northern Sweden	ACPOP	Study-wide	600	A=0.912	G=0.088
Qatari	Global	Study-wide	216	A=0.866	G=0.134
SGDP_PRJ	Global	Study-wide	208	A=0.370	G=0.630
The Danish reference pan genome	Danish	Study-wide	40	A=0.88	G=0.12

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 4	NC_000004.12:g.99115364A>C
GRCh38.p14 chr 4	NC_000004.12:g.99115364A>G
GRCh38.p14 chr 4	NC_000004.12:g.99115364A>T
GRCh37.p13 chr 4	NC_000004.11:g.100036515A>C
GRCh37.p13 chr 4	NC_000004.11:g.100036515A>G
GRCh37.p13 chr 4	NC_000004.11:g.100036515A>T

Gene: LOC100507053, uncharacterized LOC100507053 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC100507053 transcript	NR_037884.1:n.	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.

Not Reported in ClinVar

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=	C	G	T
GRCh38.p14 chr 4	NC_000004.12:g.99115364=	NC_000004.12:g.99115364A>C	NC_000004.12:g.99115364A>G	NC_000004.12:g.99115364A>T
GRCh37.p13 chr 4	NC_000004.11:g.100036515=	NC_000004.11:g.100036515A>C	NC_000004.11:g.100036515A>G	NC_000004.11:g.100036515A>T

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#.

34 SubSNP, 15 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	BCM-HGSC-SUB	ss206630944	Jul 04, 2010 (132)
2	GMI	ss277844001	May 04, 2012 (142)
3	1000GENOMES	ss331831743	May 09, 2011 (142)
4	MPI_MOLGEN	ss469146739	Sep 17, 2011 (142)
5	SSMP	ss651525110	Apr 25, 2013 (142)
6	EVA-GONL	ss980449062	Aug 21, 2014 (142)
7	1000GENOMES	ss1310976665	Aug 21, 2014 (142)
8	EVA_GENOME_DK	ss1580686918	Apr 01, 2015 (144)
9	WEILL_CORNELL_DGM	ss1923689248	Feb 12, 2016 (147)
10	JJLAB	ss2022430471	Sep 14, 2016 (149)
11	GRF	ss2706036690	Nov 08, 2017 (151)
12	GNOMAD	ss2812844997	Nov 08, 2017 (151)
13	AFFY	ss2985926518	Nov 08, 2017 (151)
14	SWEGEN	ss2995208999	Nov 08, 2017 (151)
15	CSHL	ss3345861272	Nov 08, 2017 (151)
16	EGCUT_WGS	ss3663104711	Jul 13, 2019 (153)
17	ACPOP	ss3731420902	Jul 13, 2019 (153)
18	EVA	ss3762166167	Jul 13, 2019 (153)
19	KHV_HUMAN_GENOMES	ss3805314486	Jul 13, 2019 (153)
20	SGDP_PRJ	ss3859608931	Apr 26, 2020 (154)
21	KRGDB	ss3905886301	Apr 26, 2020 (154)
22	KOGIC	ss3954740947	Apr 26, 2020 (154)
23	TOPMED	ss4624610160	Apr 26, 2021 (155)
24	TOMMO_GENOMICS	ss5167075055	Apr 26, 2021 (155)
25	1000G_HIGH_COVERAGE	ss5260285936	Oct 13, 2022 (156)
26	EVA	ss5350971575	Oct 13, 2022 (156)
27	EVA	ss5507640923	Oct 13, 2022 (156)
28	1000G_HIGH_COVERAGE	ss5541952237	Oct 13, 2022 (156)
29	SANFORD_IMAGENETICS	ss5635664039	Oct 13, 2022 (156)
30	TOMMO_GENOMICS	ss5701805277	Oct 13, 2022 (156)
31	YY_MCH	ss5805353410	Oct 13, 2022 (156)
32	EVA	ss5844422933	Oct 13, 2022 (156)
33	EVA	ss5864673960	Oct 13, 2022 (156)
34	EVA	ss5964054627	Oct 13, 2022 (156)
35	1000Genomes	NC_000004.11 - 100036515	Oct 12, 2018 (152)
36	1000Genomes_30x	NC_000004.12 - 99115364	Oct 13, 2022 (156)
37	Genetic variation in the Estonian population	NC_000004.11 - 100036515	Oct 12, 2018 (152)
38	The Danish reference pan genome	NC_000004.11 - 100036515	Apr 26, 2020 (154)
39	gnomAD - Genomes	NC_000004.12 - 99115364	Apr 26, 2021 (155)
40	Genome of the Netherlands Release 5	NC_000004.11 - 100036515	Apr 26, 2020 (154)
41	KOREAN population from KRGDB	NC_000004.11 - 100036515	Apr 26, 2020 (154)
42	Korean Genome Project	NC_000004.12 - 99115364	Apr 26, 2020 (154)
43	Northern Sweden	NC_000004.11 - 100036515	Jul 13, 2019 (153)
44	Qatari	NC_000004.11 - 100036515	Apr 26, 2020 (154)
45	SGDP_PRJ	NC_000004.11 - 100036515	Apr 26, 2020 (154)
46	8.3KJPN	NC_000004.11 - 100036515	Apr 26, 2021 (155)
47	14KJPN	NC_000004.12 - 99115364	Oct 13, 2022 (156)
48	TopMed	NC_000004.12 - 99115364	Apr 26, 2021 (155)
49	ALFA	NC_000004.12 - 99115364	Apr 26, 2021 (155)

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)
rs145724447	Aug 21, 2014 (142)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
13063695, ss3905886301	NC_000004.11:100036514:A:C	NC_000004.12:99115363:A:C	(self)
ss206630944, ss277844001, ss469146739	NC_000004.10:100255537:A:G	NC_000004.12:99115363:A:G	(self)
22418727, 8842959, 6851857, 5512559, 13063695, 4705767, 5731178, 11625911, 25044362, ss331831743, ss651525110, ss980449062, ss1310976665, ss1580686918, ss1923689248, ss2022430471, ss2706036690, ss2812844997, ss2985926518, ss2995208999, ss3345861272, ss3663104711, ss3731420902, ss3762166167, ss3859608931, ss3905886301, ss5167075055, ss5350971575, ss5507640923, ss5635664039, ss5844422933, ss5964054627	NC_000004.11:100036514:A:G	NC_000004.12:99115363:A:G	(self)
29478172, 158809394, 11118948, 35642381, 461987716, 617366619, ss3805314486, ss3954740947, ss4624610160, ss5260285936, ss5541952237, ss5701805277, ss5805353410, ss5864673960	NC_000004.12:99115363:A:G	NC_000004.12:99115363:A:G	(self)
13063695, ss3905886301	NC_000004.11:100036514:A:T	NC_000004.12:99115363:A:T	(self)

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

No publications for rs111419170

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

rs111419170