Name: rs138293424
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.

rs138293424

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:99194223 (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=0.116283 (30779/264690, TOPMED)
T=0.104726 (14407/137568, GnomAD)
T=0.07873 (2224/28250, 14KJPN) (+ 15 more)
T=0.08568 (1618/18884, ALFA)
T=0.07550 (1265/16756, 8.3KJPN)
T=0.1254 (803/6404, 1000G_30x)
T=0.1200 (601/5008, 1000G)
T=0.0568 (254/4474, Estonian)
T=0.0825 (318/3854, ALSPAC)
T=0.0882 (327/3708, TWINSUK)
T=0.1232 (360/2922, KOREAN)
T=0.1081 (198/1832, Korea1K)
T=0.088 (88/998, GoNL)
T=0.108 (65/600, NorthernSweden)
T=0.106 (23/216, Qatari)
C=0.395 (68/172, SGDP_PRJ)
T=0.12 (5/40, GENOME_DK)
C=0.32 (7/22, Siberian)

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: 20230706150541

Population	Group	Sample Size	Ref Allele	Alt Allele
Total	Global	18884	C=0.91432	T=0.08568
European	Sub	14280	C=0.92878	T=0.07122
African	Sub	2946	C=0.9016	T=0.0984
African Others	Sub	114	C=0.877	T=0.123
African American	Sub	2832	C=0.9025	T=0.0975
Asian	Sub	112	C=0.946	T=0.054
East Asian	Sub	86	C=0.94	T=0.06
Other Asian	Sub	26	C=0.96	T=0.04
Latin American 1	Sub	146	C=0.877	T=0.123
Latin American 2	Sub	610	C=0.669	T=0.331
South Asian	Sub	98	C=0.97	T=0.03
Other	Sub	692	C=0.882	T=0.118

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=0.883717	T=0.116283
gnomAD - Genomes	Global	Study-wide	137568	C=0.895274	T=0.104726
gnomAD - Genomes	European	Sub	74880	C=0.91426	T=0.08574
gnomAD - Genomes	African	Sub	40760	C=0.90211	T=0.09789
gnomAD - Genomes	American	Sub	13404	C=0.76373	T=0.23627
gnomAD - Genomes	Ashkenazi Jewish	Sub	3308	C=0.9111	T=0.0889
gnomAD - Genomes	East Asian	Sub	3110	C=0.9000	T=0.1000
gnomAD - Genomes	Other	Sub	2106	C=0.8932	T=0.1068
14KJPN	JAPANESE	Study-wide	28250	C=0.92127	T=0.07873
Allele Frequency Aggregator	Total	Global	18884	C=0.91432	T=0.08568
Allele Frequency Aggregator	European	Sub	14280	C=0.92878	T=0.07122
Allele Frequency Aggregator	African	Sub	2946	C=0.9016	T=0.0984
Allele Frequency Aggregator	Other	Sub	692	C=0.882	T=0.118
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.669	T=0.331
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.877	T=0.123
Allele Frequency Aggregator	Asian	Sub	112	C=0.946	T=0.054
Allele Frequency Aggregator	South Asian	Sub	98	C=0.97	T=0.03
8.3KJPN	JAPANESE	Study-wide	16756	C=0.92450	T=0.07550
1000Genomes_30x	Global	Study-wide	6404	C=0.8746	T=0.1254
1000Genomes_30x	African	Sub	1786	C=0.8942	T=0.1058
1000Genomes_30x	Europe	Sub	1266	C=0.9060	T=0.0940
1000Genomes_30x	South Asian	Sub	1202	C=0.9617	T=0.0383
1000Genomes_30x	East Asian	Sub	1170	C=0.8932	T=0.1068
1000Genomes_30x	American	Sub	980	C=0.669	T=0.331
1000Genomes	Global	Study-wide	5008	C=0.8800	T=0.1200
1000Genomes	African	Sub	1322	C=0.8911	T=0.1089
1000Genomes	East Asian	Sub	1008	C=0.8998	T=0.1002
1000Genomes	Europe	Sub	1006	C=0.9076	T=0.0924
1000Genomes	South Asian	Sub	978	C=0.962	T=0.038
1000Genomes	American	Sub	694	C=0.674	T=0.326
Genetic variation in the Estonian population	Estonian	Study-wide	4474	C=0.9432	T=0.0568
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.9175	T=0.0825
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.9118	T=0.0882
KOREAN population from KRGDB	KOREAN	Study-wide	2922	C=0.8768	T=0.1232
Korean Genome Project	KOREAN	Study-wide	1832	C=0.8919	T=0.1081
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.912	T=0.088
Northern Sweden	ACPOP	Study-wide	600	C=0.892	T=0.108
Qatari	Global	Study-wide	216	C=0.894	T=0.106
SGDP_PRJ	Global	Study-wide	172	C=0.395	T=0.605
The Danish reference pan genome	Danish	Study-wide	40	C=0.88	T=0.12
Siberian	Global	Study-wide	22	C=0.32	T=0.68

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.99194223C>T
GRCh37.p13 chr 4	NC_000004.11:g.100115380C>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	C=	T
GRCh38.p14 chr 4	NC_000004.12:g.99194223=	NC_000004.12:g.99194223C>T
GRCh37.p13 chr 4	NC_000004.11:g.100115380=	NC_000004.11:g.100115380C>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#.

46 SubSNP, 18 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	GMI	ss277844255	May 04, 2012 (137)
2	1000GENOMES	ss331831993	May 09, 2011 (134)
3	TISHKOFF	ss557720952	Apr 25, 2013 (138)
4	SSMP	ss651525516	Apr 25, 2013 (138)
5	EVA-GONL	ss980449744	Aug 21, 2014 (142)
6	JMKIDD_LAB	ss1071786907	Aug 21, 2014 (142)
7	1000GENOMES	ss1310978718	Aug 21, 2014 (142)
8	DDI	ss1429982590	Apr 01, 2015 (144)
9	EVA_GENOME_DK	ss1580687282	Apr 01, 2015 (144)
10	EVA_DECODE	ss1589953767	Apr 01, 2015 (144)
11	EVA_UK10K_ALSPAC	ss1610735583	Apr 01, 2015 (144)
12	EVA_UK10K_TWINSUK	ss1653729616	Apr 01, 2015 (144)
13	WEILL_CORNELL_DGM	ss1923689882	Feb 12, 2016 (147)
14	JJLAB	ss2022430879	Sep 14, 2016 (149)
15	USC_VALOUEV	ss2150560042	Dec 20, 2016 (150)
16	HUMAN_LONGEVITY	ss2265422572	Dec 20, 2016 (150)
17	GRF	ss2706036959	Nov 08, 2017 (151)
18	GNOMAD	ss2812850816	Nov 08, 2017 (151)
19	SWEGEN	ss2995209994	Nov 08, 2017 (151)
20	BIOINF_KMB_FNS_UNIBA	ss3024990694	Nov 08, 2017 (151)
21	CSHL	ss3345861653	Nov 08, 2017 (151)
22	EGCUT_WGS	ss3663105731	Jul 13, 2019 (153)
23	EVA_DECODE	ss3712656249	Jul 13, 2019 (153)
24	ACPOP	ss3731421533	Jul 13, 2019 (153)
25	EVA	ss3762166776	Jul 13, 2019 (153)
26	KHV_HUMAN_GENOMES	ss3805315178	Jul 13, 2019 (153)
27	EVA	ss3828703379	Apr 26, 2020 (154)
28	EVA	ss3837792729	Apr 26, 2020 (154)
29	EVA	ss3843231117	Apr 26, 2020 (154)
30	SGDP_PRJ	ss3859610061	Apr 26, 2020 (154)
31	KRGDB	ss3905887416	Apr 26, 2020 (154)
32	KOGIC	ss3954741830	Apr 26, 2020 (154)
33	TOPMED	ss4624628699	Apr 26, 2021 (155)
34	TOMMO_GENOMICS	ss5167077214	Apr 26, 2021 (155)
35	1000G_HIGH_COVERAGE	ss5260287629	Oct 13, 2022 (156)
36	EVA	ss5350974614	Oct 13, 2022 (156)
37	HUGCELL_USP	ss5458930151	Oct 13, 2022 (156)
38	EVA	ss5507641333	Oct 13, 2022 (156)
39	1000G_HIGH_COVERAGE	ss5541954890	Oct 13, 2022 (156)
40	SANFORD_IMAGENETICS	ss5635665073	Oct 13, 2022 (156)
41	TOMMO_GENOMICS	ss5701808094	Oct 13, 2022 (156)
42	YY_MCH	ss5805353804	Oct 13, 2022 (156)
43	EVA	ss5844423792	Oct 13, 2022 (156)
44	EVA	ss5854355855	Oct 13, 2022 (156)
45	EVA	ss5864675970	Oct 13, 2022 (156)
46	EVA	ss5964055708	Oct 13, 2022 (156)
47	1000Genomes	NC_000004.11 - 100115380	Oct 12, 2018 (152)
48	1000Genomes_30x	NC_000004.12 - 99194223	Oct 13, 2022 (156)
49	The Avon Longitudinal Study of Parents and Children	NC_000004.11 - 100115380	Oct 12, 2018 (152)
50	Genetic variation in the Estonian population	NC_000004.11 - 100115380	Oct 12, 2018 (152)
51	The Danish reference pan genome	NC_000004.11 - 100115380	Apr 26, 2020 (154)
52	gnomAD - Genomes	NC_000004.12 - 99194223	Apr 26, 2021 (155)
53	Genome of the Netherlands Release 5	NC_000004.11 - 100115380	Apr 26, 2020 (154)
54	KOREAN population from KRGDB	NC_000004.11 - 100115380	Apr 26, 2020 (154)
55	Korean Genome Project	NC_000004.12 - 99194223	Apr 26, 2020 (154)
56	Northern Sweden	NC_000004.11 - 100115380	Jul 13, 2019 (153)
57	Qatari	NC_000004.11 - 100115380	Apr 26, 2020 (154)
58	SGDP_PRJ	NC_000004.11 - 100115380	Apr 26, 2020 (154)
59	Siberian	NC_000004.11 - 100115380	Apr 26, 2020 (154)
60	8.3KJPN	NC_000004.11 - 100115380	Apr 26, 2021 (155)
61	14KJPN	NC_000004.12 - 99194223	Oct 13, 2022 (156)
62	TopMed	NC_000004.12 - 99194223	Apr 26, 2021 (155)
63	UK 10K study - Twins	NC_000004.11 - 100115380	Oct 12, 2018 (152)
64	ALFA	NC_000004.12 - 99194223	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss277844255, ss1589953767	NC_000004.10:100334402:C:T	NC_000004.12:99194222:C:T	(self)
22420866, 12471723, 8843979, 6852221, 5513228, 13064810, 4706398, 5731812, 11627041, 3076396, 25046521, 12471723, ss331831993, ss557720952, ss651525516, ss980449744, ss1071786907, ss1310978718, ss1429982590, ss1580687282, ss1610735583, ss1653729616, ss1923689882, ss2022430879, ss2150560042, ss2706036959, ss2812850816, ss2995209994, ss3345861653, ss3663105731, ss3731421533, ss3762166776, ss3828703379, ss3837792729, ss3859610061, ss3905887416, ss5167077214, ss5350974614, ss5507641333, ss5635665073, ss5844423792, ss5964055708	NC_000004.11:100115379:C:T	NC_000004.12:99194222:C:T	(self)
29480825, 158824515, 11119831, 35645198, 462006255, 789298068, ss2265422572, ss3024990694, ss3712656249, ss3805315178, ss3843231117, ss3954741830, ss4624628699, ss5260287629, ss5458930151, ss5541954890, ss5701808094, ss5805353804, ss5854355855, ss5864675970	NC_000004.12:99194222:C:T	NC_000004.12:99194222:C: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 rs138293424

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

rs138293424