Name: rs16976358
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.

rs16976358

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr18:42611606 (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: T>C
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.012207 (3231/264690, TOPMED)
C=0.009876 (1385/140246, GnomAD)
C=0.11087 (3133/28258, 14KJPN) (+ 18 more)
C=0.00809 (160/19768, ALFA)
C=0.11325 (1898/16760, 8.3KJPN)
C=0.0458 (293/6404, 1000G_30x)
C=0.0477 (239/5008, 1000G)
C=0.0036 (16/4480, Estonian)
C=0.0073 (28/3854, ALSPAC)
C=0.0076 (28/3708, TWINSUK)
C=0.1403 (410/2922, KOREAN)
C=0.1528 (280/1832, Korea1K)
C=0.0545 (77/1412, HapMap)
C=0.003 (3/998, GoNL)
C=0.002 (1/626, Chileans)
C=0.012 (7/600, NorthernSweden)
C=0.245 (53/216, Vietnamese)
T=0.38 (38/100, SGDP_PRJ)
C=0.03 (1/40, GENOME_DK)
T=0.5 (3/6, Siberian)
C=0.5 (3/6, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LINC00907 : Intron 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	19768	T=0.99191	C=0.00809
European	Sub	13598	T=0.99507	C=0.00493
African	Sub	3564	T=0.9949	C=0.0051
African Others	Sub	120	T=1.000	C=0.000
African American	Sub	3444	T=0.9948	C=0.0052
Asian	Sub	160	T=0.731	C=0.269
East Asian	Sub	102	T=0.755	C=0.245
Other Asian	Sub	58	T=0.69	C=0.31
Latin American 1	Sub	220	T=0.991	C=0.009
Latin American 2	Sub	760	T=0.993	C=0.007
South Asian	Sub	106	T=0.972	C=0.028
Other	Sub	1360	T=0.9838	C=0.0162

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	T=0.987793	C=0.012207
gnomAD - Genomes	Global	Study-wide	140246	T=0.990124	C=0.009876
gnomAD - Genomes	European	Sub	75950	T=0.99280	C=0.00720
gnomAD - Genomes	African	Sub	42042	T=0.99698	C=0.00302
gnomAD - Genomes	American	Sub	13652	T=0.99568	C=0.00432
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	T=0.9934	C=0.0066
gnomAD - Genomes	East Asian	Sub	3128	T=0.8130	C=0.1870
gnomAD - Genomes	Other	Sub	2150	T=0.9791	C=0.0209
14KJPN	JAPANESE	Study-wide	28258	T=0.88913	C=0.11087
Allele Frequency Aggregator	Total	Global	19768	T=0.99191	C=0.00809
Allele Frequency Aggregator	European	Sub	13598	T=0.99507	C=0.00493
Allele Frequency Aggregator	African	Sub	3564	T=0.9949	C=0.0051
Allele Frequency Aggregator	Other	Sub	1360	T=0.9838	C=0.0162
Allele Frequency Aggregator	Latin American 2	Sub	760	T=0.993	C=0.007
Allele Frequency Aggregator	Latin American 1	Sub	220	T=0.991	C=0.009
Allele Frequency Aggregator	Asian	Sub	160	T=0.731	C=0.269
Allele Frequency Aggregator	South Asian	Sub	106	T=0.972	C=0.028
8.3KJPN	JAPANESE	Study-wide	16760	T=0.88675	C=0.11325
1000Genomes_30x	Global	Study-wide	6404	T=0.9542	C=0.0458
1000Genomes_30x	African	Sub	1786	T=0.9989	C=0.0011
1000Genomes_30x	Europe	Sub	1266	T=0.9937	C=0.0063
1000Genomes_30x	South Asian	Sub	1202	T=0.9784	C=0.0216
1000Genomes_30x	East Asian	Sub	1170	T=0.7812	C=0.2188
1000Genomes_30x	American	Sub	980	T=0.999	C=0.001
1000Genomes	Global	Study-wide	5008	T=0.9523	C=0.0477
1000Genomes	African	Sub	1322	T=0.9985	C=0.0015
1000Genomes	East Asian	Sub	1008	T=0.7937	C=0.2063
1000Genomes	Europe	Sub	1006	T=0.9930	C=0.0070
1000Genomes	South Asian	Sub	978	T=0.979	C=0.021
1000Genomes	American	Sub	694	T=0.999	C=0.001
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.9964	C=0.0036
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.9927	C=0.0073
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.9924	C=0.0076
KOREAN population from KRGDB	KOREAN	Study-wide	2922	T=0.8597	C=0.1403
Korean Genome Project	KOREAN	Study-wide	1832	T=0.8472	C=0.1528
HapMap	Global	Study-wide	1412	T=0.9455	C=0.0545
HapMap	African	Sub	586	T=0.997	C=0.003
HapMap	American	Sub	572	T=0.941	C=0.059
HapMap	Asian	Sub	254	T=0.839	C=0.161
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.997	C=0.003
Chileans	Chilean	Study-wide	626	T=0.998	C=0.002
Northern Sweden	ACPOP	Study-wide	600	T=0.988	C=0.012
A Vietnamese Genetic Variation Database	Global	Study-wide	216	T=0.755	C=0.245
SGDP_PRJ	Global	Study-wide	100	T=0.38	C=0.62
The Danish reference pan genome	Danish	Study-wide	40	T=0.97	C=0.03
Siberian	Global	Study-wide	6	T=0.5	C=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 18	NC_000018.10:g.42611606T>C
GRCh37.p13 chr 18	NC_000018.9:g.40191571T>C

Gene: LINC00907, long intergenic non-protein coding RNA 907 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LINC00907 transcript variant 1	NR_046174.2:n.	N/A	Intron Variant
LINC00907 transcript variant 2	NR_046454.1:n.	N/A	Genic Downstream Transcript Variant
LINC00907 transcript variant 4	NR_046456.1:n.	N/A	Genic Downstream Transcript Variant
LINC00907 transcript variant 5	NR_046457.1:n.	N/A	Genic Downstream Transcript Variant
LINC00907 transcript variant 6	NR_046458.1: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	T=	C
GRCh38.p14 chr 18	NC_000018.10:g.42611606=	NC_000018.10:g.42611606T>C
GRCh37.p13 chr 18	NC_000018.9:g.40191571=	NC_000018.9:g.40191571T>C

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#.

47 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	PERLEGEN	ss24030619	Sep 20, 2004 (123)
2	AFFY	ss66310470	Dec 01, 2006 (127)
3	AFFY	ss75990009	Dec 07, 2007 (129)
4	KRIBB_YJKIM	ss83133375	Dec 15, 2007 (130)
5	BGI	ss103391100	Dec 01, 2009 (131)
6	AFFY	ss170091165	Jul 04, 2010 (132)
7	1000GENOMES	ss243702782	Jul 15, 2010 (132)
8	GMI	ss282975372	May 04, 2012 (137)
9	ILLUMINA	ss534068842	Sep 08, 2015 (146)
10	SSMP	ss661447225	Apr 25, 2013 (138)
11	EVA-GONL	ss993687411	Aug 21, 2014 (142)
12	JMKIDD_LAB	ss1081470767	Aug 21, 2014 (142)
13	1000GENOMES	ss1360876071	Aug 21, 2014 (142)
14	EVA_GENOME_DK	ss1578386655	Apr 01, 2015 (144)
15	EVA_UK10K_ALSPAC	ss1636790702	Apr 01, 2015 (144)
16	EVA_UK10K_TWINSUK	ss1679784735	Apr 01, 2015 (144)
17	EVA_DECODE	ss1697743987	Apr 01, 2015 (144)
18	EVA_SVP	ss1713622928	Apr 01, 2015 (144)
19	USC_VALOUEV	ss2157851802	Dec 20, 2016 (150)
20	HUMAN_LONGEVITY	ss2221261827	Dec 20, 2016 (150)
21	SYSTEMSBIOZJU	ss2629171840	Nov 08, 2017 (151)
22	GRF	ss2702437648	Nov 08, 2017 (151)
23	GNOMAD	ss2956268267	Nov 08, 2017 (151)
24	SWEGEN	ss3016465768	Nov 08, 2017 (151)
25	ILLUMINA	ss3627800148	Oct 12, 2018 (152)
26	EGCUT_WGS	ss3683304346	Jul 13, 2019 (153)
27	EVA_DECODE	ss3701585099	Jul 13, 2019 (153)
28	ACPOP	ss3742510561	Jul 13, 2019 (153)
29	EVA	ss3755341196	Jul 13, 2019 (153)
30	KHV_HUMAN_GENOMES	ss3820606237	Jul 13, 2019 (153)
31	SGDP_PRJ	ss3886942447	Apr 27, 2020 (154)
32	KRGDB	ss3936804198	Apr 27, 2020 (154)
33	KOGIC	ss3980079333	Apr 27, 2020 (154)
34	TOPMED	ss5055382158	Apr 26, 2021 (155)
35	TOMMO_GENOMICS	ss5225004305	Apr 26, 2021 (155)
36	1000G_HIGH_COVERAGE	ss5305165120	Oct 16, 2022 (156)
37	EVA	ss5431183279	Oct 16, 2022 (156)
38	HUGCELL_USP	ss5497949001	Oct 16, 2022 (156)
39	EVA	ss5511924457	Oct 16, 2022 (156)
40	1000G_HIGH_COVERAGE	ss5609940026	Oct 16, 2022 (156)
41	SANFORD_IMAGENETICS	ss5661222676	Oct 16, 2022 (156)
42	TOMMO_GENOMICS	ss5782747979	Oct 16, 2022 (156)
43	YY_MCH	ss5817064217	Oct 16, 2022 (156)
44	EVA	ss5827492301	Oct 16, 2022 (156)
45	EVA	ss5852037109	Oct 16, 2022 (156)
46	EVA	ss5873932565	Oct 16, 2022 (156)
47	EVA	ss5952632057	Oct 16, 2022 (156)
48	1000Genomes	NC_000018.9 - 40191571	Oct 12, 2018 (152)
49	1000Genomes_30x	NC_000018.10 - 42611606	Oct 16, 2022 (156)
50	The Avon Longitudinal Study of Parents and Children	NC_000018.9 - 40191571	Oct 12, 2018 (152)
51	Chileans	NC_000018.9 - 40191571	Apr 27, 2020 (154)
52	Genetic variation in the Estonian population	NC_000018.9 - 40191571	Oct 12, 2018 (152)
53	The Danish reference pan genome	NC_000018.9 - 40191571	Apr 27, 2020 (154)
54	gnomAD - Genomes	NC_000018.10 - 42611606	Apr 26, 2021 (155)
55	Genome of the Netherlands Release 5	NC_000018.9 - 40191571	Apr 27, 2020 (154)
56	HapMap	NC_000018.10 - 42611606	Apr 27, 2020 (154)
57	KOREAN population from KRGDB	NC_000018.9 - 40191571	Apr 27, 2020 (154)
58	Korean Genome Project	NC_000018.10 - 42611606	Apr 27, 2020 (154)
59	Northern Sweden	NC_000018.9 - 40191571	Jul 13, 2019 (153)
60	SGDP_PRJ	NC_000018.9 - 40191571	Apr 27, 2020 (154)
61	Siberian	NC_000018.9 - 40191571	Apr 27, 2020 (154)
62	8.3KJPN	NC_000018.9 - 40191571	Apr 26, 2021 (155)
63	14KJPN	NC_000018.10 - 42611606	Oct 16, 2022 (156)
64	TopMed	NC_000018.10 - 42611606	Apr 26, 2021 (155)
65	UK 10K study - Twins	NC_000018.9 - 40191571	Oct 12, 2018 (152)
66	A Vietnamese Genetic Variation Database	NC_000018.9 - 40191571	Jul 13, 2019 (153)
67	ALFA	NC_000018.10 - 42611606	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)
rs59654398	Feb 27, 2009 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss282975372, ss1697743987, ss1713622928	NC_000018.8:38445568:T:C	NC_000018.10:42611605:T:C	(self)
74200379, 41106445, 194058, 29042594, 4579384, 18315817, 43981592, 15795426, 38959427, 10368156, 82973612, 41106445, 9082829, ss243702782, ss534068842, ss661447225, ss993687411, ss1081470767, ss1360876071, ss1578386655, ss1636790702, ss1679784735, ss2157851802, ss2629171840, ss2702437648, ss2956268267, ss3016465768, ss3627800148, ss3683304346, ss3742510561, ss3755341196, ss3886942447, ss3936804198, ss5225004305, ss5431183279, ss5511924457, ss5661222676, ss5827492301, ss5952632057	NC_000018.9:40191570:T:C	NC_000018.10:42611605:T:C	(self)
97465961, 523465330, 1593965, 36457334, 116585083, 270927821, 12518430421, ss2221261827, ss3701585099, ss3820606237, ss3980079333, ss5055382158, ss5305165120, ss5497949001, ss5609940026, ss5782747979, ss5817064217, ss5852037109, ss5873932565	NC_000018.10:42611605:T:C	NC_000018.10:42611605:T:C	(self)
ss24030619, ss66310470, ss75990009, ss83133375, ss103391100, ss170091165	NT_010966.14:21680672:T:C	NC_000018.10:42611605:T:C	(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 rs16976358

PMID	Title	Author	Year	Journal
26314684	Genome-wide Association Study of Autism Spectrum Disorder in the East Asian Populations.	Liu X et al.	2016	Autism research
28190241	Ras-like without CAAX 2 (RIT2): a susceptibility gene for autism spectrum disorder.	Hamedani SY et al.	2017	Metabolic brain disease

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

rs16976358