Name: rs72699384
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.

rs72699384

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr9:105362 (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: A=0.000007 (1/139966, GnomAD)
C=0.50000 (14129/28258, 14KJPN)
T=0.50000 (14129/28258, 14KJPN) (+ 12 more)
T=0.49994 (8379/16760, 8.3KJPN)
C=0.5000 (3202/6404, 1000G_30x)
T=0.5000 (3202/6404, 1000G_30x)
T=0.4996 (2234/4472, ALFA)
T=0.4966 (1455/2930, KOREAN)
T=0.4934 (897/1818, Korea1K)
C=0.500 (279/558, SGDP_PRJ)
T=0.500 (279/558, SGDP_PRJ)
C=0.500 (108/216, Qatari)
T=0.500 (108/216, Qatari)
C=0.50 (28/56, Siberian)
T=0.50 (28/56, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LINC01388 : 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	4472	C=0.5004	A=0.0000, G=0.0000, T=0.4996
European	Sub	4464	C=0.5004	A=0.0000, G=0.0000, T=0.4996
African	Sub	0	C=0	A=0, G=0, T=0
African Others	Sub	0	C=0	A=0, G=0, T=0
African American	Sub	0	C=0	A=0, G=0, T=0
Asian	Sub	0	C=0	A=0, G=0, T=0
East Asian	Sub	0	C=0	A=0, G=0, T=0
Other Asian	Sub	0	C=0	A=0, G=0, T=0
Latin American 1	Sub	0	C=0	A=0, G=0, T=0
Latin American 2	Sub	0	C=0	A=0, G=0, T=0
South Asian	Sub	0	C=0	A=0, G=0, T=0
Other	Sub	8	C=0.5	A=0.0, G=0.0, T=0.5

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
gnomAD - Genomes	Global	Study-wide	139966	C=0.999993	A=0.000007
gnomAD - Genomes	European	Sub	75748	C=0.99999	A=0.00001
gnomAD - Genomes	African	Sub	41996	C=1.00000	A=0.00000
gnomAD - Genomes	American	Sub	13616	C=1.00000	A=0.00000
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	C=1.0000	A=0.0000
gnomAD - Genomes	East Asian	Sub	3132	C=1.0000	A=0.0000
gnomAD - Genomes	Other	Sub	2152	C=1.0000	A=0.0000
14KJPN	JAPANESE	Study-wide	28258	C=0.50000	T=0.50000
8.3KJPN	JAPANESE	Study-wide	16760	C=0.50006	T=0.49994
1000Genomes_30x	Global	Study-wide	6404	C=0.5000	T=0.5000
1000Genomes_30x	African	Sub	1786	C=0.5000	T=0.5000
1000Genomes_30x	Europe	Sub	1266	C=0.5000	T=0.5000
1000Genomes_30x	South Asian	Sub	1202	C=0.5000	T=0.5000
1000Genomes_30x	East Asian	Sub	1170	C=0.5000	T=0.5000
1000Genomes_30x	American	Sub	980	C=0.500	T=0.500
Allele Frequency Aggregator	Total	Global	4472	C=0.5004	A=0.0000, G=0.0000, T=0.4996
Allele Frequency Aggregator	European	Sub	4464	C=0.5004	A=0.0000, G=0.0000, T=0.4996
Allele Frequency Aggregator	Other	Sub	8	C=0.5	A=0.0, G=0.0, T=0.5
Allele Frequency Aggregator	Latin American 1	Sub	0	C=0	A=0, G=0, T=0
Allele Frequency Aggregator	Latin American 2	Sub	0	C=0	A=0, G=0, T=0
Allele Frequency Aggregator	South Asian	Sub	0	C=0	A=0, G=0, T=0
Allele Frequency Aggregator	African	Sub	0	C=0	A=0, G=0, T=0
Allele Frequency Aggregator	Asian	Sub	0	C=0	A=0, G=0, T=0
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.5034	T=0.4966
Korean Genome Project	KOREAN	Study-wide	1818	C=0.5066	T=0.4934
SGDP_PRJ	Global	Study-wide	558	C=0.500	T=0.500
Qatari	Global	Study-wide	216	C=0.500	T=0.500
Siberian	Global	Study-wide	56	C=0.50	T=0.50

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.105362C>A
GRCh38.p14 chr 9	NC_000009.12:g.105362C>G
GRCh38.p14 chr 9	NC_000009.12:g.105362C>T
GRCh37.p13 chr 9	NC_000009.11:g.105362C>A
GRCh37.p13 chr 9	NC_000009.11:g.105362C>G
GRCh37.p13 chr 9	NC_000009.11:g.105362C>T

Gene: LINC01388, uncharacterized LINC01388 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LINC01388 transcript variant X2	XR_007061384.1:n.	N/A	Intron Variant
LINC01388 transcript variant X3	XR_007061385.1:n.	N/A	Intron Variant
LINC01388 transcript variant X6	XR_007061386.1:n.	N/A	Intron Variant
LINC01388 transcript variant X7	XR_007061387.1:n.	N/A	Intron Variant
LINC01388 transcript variant X8	XR_007061388.1:n.	N/A	Intron Variant
LINC01388 transcript variant X4	XR_929388.3:n.	N/A	Intron Variant
LINC01388 transcript variant X5	XR_929390.3:n.	N/A	Intron Variant
LINC01388 transcript variant X1	XR_929387.3:n.	N/A	Genic Downstream Transcript 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=	A	G	T
GRCh38.p14 chr 9	NC_000009.12:g.105362=	NC_000009.12:g.105362C>A	NC_000009.12:g.105362C>G	NC_000009.12:g.105362C>T
GRCh37.p13 chr 9	NC_000009.11:g.105362=	NC_000009.11:g.105362C>A	NC_000009.11:g.105362C>G	NC_000009.11:g.105362C>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#.

25 SubSNP, 10 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	1000GENOMES	ss108503407	Feb 13, 2009 (130)
2	ILLUMINA-UK	ss115669604	Dec 01, 2009 (131)
3	BCM-HGSC-SUB	ss206892444	Jul 04, 2010 (132)
4	1000GENOMES	ss210685812	Jul 14, 2010 (132)
5	GMI	ss280060297	May 04, 2012 (137)
6	GMI	ss285950333	Apr 25, 2013 (138)
7	SSMP	ss655596726	Apr 25, 2013 (138)
8	DDI	ss1431715351	Apr 01, 2015 (144)
9	WEILL_CORNELL_DGM	ss1929478029	Feb 12, 2016 (147)
10	GENOMED	ss1971128370	Jul 19, 2016 (147)
11	USC_VALOUEV	ss2153676780	Dec 20, 2016 (150)
12	GRF	ss2709469651	Nov 08, 2017 (151)
13	GNOMAD	ss2874247581	Nov 08, 2017 (151)
14	SWEGEN	ss3004221324	Nov 08, 2017 (151)
15	BIOINF_KMB_FNS_UNIBA	ss3026510452	Nov 08, 2017 (151)
16	CSHL	ss3348473376	Nov 08, 2017 (151)
17	SGDP_PRJ	ss3871300987	Apr 26, 2020 (154)
18	KRGDB	ss3918926798	Apr 26, 2020 (154)
19	KOGIC	ss3965112541	Apr 26, 2020 (154)
20	TOMMO_GENOMICS	ss5191621253	Apr 26, 2021 (155)
21	1000G_HIGH_COVERAGE	ss5571004935	Oct 16, 2022 (156)
22	SANFORD_IMAGENETICS	ss5646694090	Oct 16, 2022 (156)
23	TOMMO_GENOMICS	ss5734542342	Oct 16, 2022 (156)
24	YY_MCH	ss5810253621	Oct 16, 2022 (156)
25	EVA	ss5828710167	Oct 16, 2022 (156)
26	1000Genomes_30x	NC_000009.12 - 105362	Oct 16, 2022 (156)
27	gnomAD - Genomes	NC_000009.12 - 105362	Apr 26, 2021 (155)
28	KOREAN population from KRGDB	NC_000009.11 - 105362	Apr 26, 2020 (154)
29	Korean Genome Project	NC_000009.12 - 105362	Apr 26, 2020 (154)
30	Qatari	NC_000009.11 - 105362	Apr 26, 2020 (154)
31	SGDP_PRJ	NC_000009.11 - 105362	Apr 26, 2020 (154)
32	Siberian	NC_000009.11 - 105362	Apr 26, 2020 (154)
33	8.3KJPN	NC_000009.11 - 105362	Apr 26, 2021 (155)
34	14KJPN	NC_000009.12 - 105362	Oct 16, 2022 (156)
35	ALFA	NC_000009.12 - 105362	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
315086200, 8071263728	NC_000009.12:105361:C:A	NC_000009.12:105361:C:A	(self)
8071263728	NC_000009.12:105361:C:G	NC_000009.12:105361:C:G	(self)
ss108503407, ss115669604, ss206892444, ss210685812, ss280060297, ss285950333	NC_000009.10:95361:C:T	NC_000009.12:105361:C:T	(self)
26104192, 11519959, 23317967, 6193134, 49590560, ss655596726, ss1431715351, ss1929478029, ss1971128370, ss2153676780, ss2709469651, ss2874247581, ss3004221324, ss3348473376, ss3871300987, ss3918926798, ss5191621253, ss5646694090, ss5828710167	NC_000009.11:105361:C:T	NC_000009.12:105361:C:T	(self)
58530870, 21490542, 68379446, 8071263728, ss3026510452, ss3965112541, ss5571004935, ss5734542342, ss5810253621	NC_000009.12:105361:C:T	NC_000009.12:105361: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 rs72699384

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

rs72699384