Name: rs11402251
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.

rs11402251

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr19:51332639 (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: dupG
Variation Type: Indel Insertion and Deletion
Frequency: G=0.001643 (435/264690, TOPMED)
G=0.000000 (0/154076, GnomAD_exome)
G=0.000000 (0/140268, GnomAD) (+ 13 more)
G=0.00000 (0/28258, 14KJPN)
G=0.00099 (25/25320, ALFA)
G=0.00000 (0/21686, ExAC)
G=0.00000 (0/16760, 8.3KJPN)
G=0.0021 (14/6758, GO-ESP)
G=0.0000 (0/6404, 1000G_30x)
G=0.0000 (0/5008, 1000G)
G=0.0000 (0/3854, ALSPAC)
G=0.0000 (0/3708, TWINSUK)
G=0.0000 (0/1832, Korea1K)
G=0.000 (0/998, GoNL)
G=0.000 (0/600, NorthernSweden)
G=0.00 (0/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: VSIG10L : Frameshift 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	25320	G=0.00099	GG=0.99901
European	Sub	18142	G=0.00121	GG=0.99879
African	Sub	3410	G=0.0009	GG=0.9991
African Others	Sub	116	G=0.000	GG=1.000
African American	Sub	3294	G=0.0009	GG=0.9991
Asian	Sub	164	G=0.000	GG=1.000
East Asian	Sub	110	G=0.000	GG=1.000
Other Asian	Sub	54	G=0.00	GG=1.00
Latin American 1	Sub	146	G=0.000	GG=1.000
Latin American 2	Sub	610	G=0.000	GG=1.000
South Asian	Sub	94	G=0.00	GG=1.00
Other	Sub	2754	G=0.0000	GG=1.0000

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	- No frequency provided	dupG=0.998357
gnomAD - Exomes	Global	Study-wide	154076	- No frequency provided	dupG=1.000000
gnomAD - Exomes	European	Sub	74994	- No frequency provided	dupG=1.00000
gnomAD - Exomes	Asian	Sub	33664	- No frequency provided	dupG=1.00000
gnomAD - Exomes	American	Sub	24666	- No frequency provided	dupG=1.00000
gnomAD - Exomes	Ashkenazi Jewish	Sub	8472	- No frequency provided	dupG=1.0000
gnomAD - Exomes	African	Sub	7912	- No frequency provided	dupG=1.0000
gnomAD - Exomes	Other	Sub	4368	- No frequency provided	dupG=1.0000
gnomAD - Genomes	Global	Study-wide	140268	- No frequency provided	dupG=1.000000
gnomAD - Genomes	European	Sub	75952	- No frequency provided	dupG=1.00000
gnomAD - Genomes	African	Sub	42052	- No frequency provided	dupG=1.00000
gnomAD - Genomes	American	Sub	13656	- No frequency provided	dupG=1.00000
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	- No frequency provided	dupG=1.0000
gnomAD - Genomes	East Asian	Sub	3130	- No frequency provided	dupG=1.0000
gnomAD - Genomes	Other	Sub	2154	- No frequency provided	dupG=1.0000
14KJPN	JAPANESE	Study-wide	28258	- No frequency provided	dupG=1.00000
Allele Frequency Aggregator	Total	Global	25320	G=0.00099	dupG=0.99901
Allele Frequency Aggregator	European	Sub	18142	G=0.00121	dupG=0.99879
Allele Frequency Aggregator	African	Sub	3410	G=0.0009	dupG=0.9991
Allele Frequency Aggregator	Other	Sub	2754	G=0.0000	dupG=1.0000
Allele Frequency Aggregator	Latin American 2	Sub	610	G=0.000	dupG=1.000
Allele Frequency Aggregator	Asian	Sub	164	G=0.000	dupG=1.000
Allele Frequency Aggregator	Latin American 1	Sub	146	G=0.000	dupG=1.000
Allele Frequency Aggregator	South Asian	Sub	94	G=0.00	dupG=1.00
ExAC	Global	Study-wide	21686	- No frequency provided	dupG=1.00000
ExAC	Europe	Sub	10372	- No frequency provided	dupG=1.00000
ExAC	Asian	Sub	8514	- No frequency provided	dupG=1.0000
ExAC	African	Sub	2148	- No frequency provided	dupG=1.0000
ExAC	American	Sub	410	- No frequency provided	dupG=1.000
ExAC	Other	Sub	242	- No frequency provided	dupG=1.000
8.3KJPN	JAPANESE	Study-wide	16760	- No frequency provided	dupG=1.00000
GO Exome Sequencing Project	Global	Study-wide	6758	- No frequency provided	dupG=0.9979
GO Exome Sequencing Project	European American	Sub	4472	- No frequency provided	dupG=0.9978
GO Exome Sequencing Project	African American	Sub	2286	- No frequency provided	dupG=0.9983
1000Genomes_30x	Global	Study-wide	6404	- No frequency provided	dupG=1.0000
1000Genomes_30x	African	Sub	1786	- No frequency provided	dupG=1.0000
1000Genomes_30x	Europe	Sub	1266	- No frequency provided	dupG=1.0000
1000Genomes_30x	South Asian	Sub	1202	- No frequency provided	dupG=1.0000
1000Genomes_30x	East Asian	Sub	1170	- No frequency provided	dupG=1.0000
1000Genomes_30x	American	Sub	980	- No frequency provided	dupG=1.000
1000Genomes	Global	Study-wide	5008	- No frequency provided	dupG=1.0000
1000Genomes	African	Sub	1322	- No frequency provided	dupG=1.0000
1000Genomes	East Asian	Sub	1008	- No frequency provided	dupG=1.0000
1000Genomes	Europe	Sub	1006	- No frequency provided	dupG=1.0000
1000Genomes	South Asian	Sub	978	- No frequency provided	dupG=1.000
1000Genomes	American	Sub	694	- No frequency provided	dupG=1.000
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	- No frequency provided	dupG=1.0000
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	- No frequency provided	dupG=1.0000
Korean Genome Project	KOREAN	Study-wide	1832	- No frequency provided	dupG=1.0000
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	- No frequency provided	dupG=1.000
Northern Sweden	ACPOP	Study-wide	600	- No frequency provided	dupG=1.000
The Danish reference pan genome	Danish	Study-wide	40	- No frequency provided	dupG=1.00

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 19	NC_000019.10:g.51332639dup
GRCh37.p13 chr 19	NC_000019.9:g.51835893dup

Gene: VSIG10L, V-set and immunoglobulin domain containing 10 like (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
VSIG10L transcript	NM_001163922.3:c.2576dup	A [GCA] > A [GCCA]	Coding Sequence Variant
V-set and immunoglobulin domain-containing protein 10-like precursor	NP_001157394.1:p.Gln860fs	A (Ala) > A (Ala)	Frameshift 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	G=	dupG
GRCh38.p14 chr 19	NC_000019.10:g.51332639=	NC_000019.10:g.51332639dup
GRCh37.p13 chr 19	NC_000019.9:g.51835893=	NC_000019.9:g.51835893dup
VSIG10L transcript	NM_001163922.3:c.2576=	NM_001163922.3:c.2576dup
VSIG10L transcript	NM_001163922.2:c.2576=	NM_001163922.2:c.2576dup
VSIG10L transcript	NM_001163922.1:c.2576=	NM_001163922.1:c.2576dup
V-set and immunoglobulin domain-containing protein 10-like precursor	NP_001157394.1:p.Ala859=	NP_001157394.1:p.Gln860fs

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#.

76 SubSNP, 16 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	DEVINE_LAB	ss15286968	Mar 15, 2016 (147)
2	HGSV	ss81110565	Dec 03, 2013 (138)
3	HGSV	ss81127346	Dec 04, 2013 (138)
4	HUMANGENOME_JCVI	ss95731538	Dec 05, 2013 (138)
5	BL	ss256208896	May 09, 2011 (138)
6	GMI	ss288528043	May 09, 2011 (138)
7	GMI	ss289393237	May 04, 2012 (138)
8	PJP	ss294966582	May 09, 2011 (135)
9	1000GENOMES	ss327913502	May 09, 2011 (138)
10	1000GENOMES	ss328038939	May 09, 2011 (138)
11	1000GENOMES	ss328280911	May 09, 2011 (138)
12	LUNTER	ss552633772	Apr 25, 2013 (138)
13	LUNTER	ss553023250	Apr 25, 2013 (138)
14	LUNTER	ss553667082	Apr 25, 2013 (138)
15	TISHKOFF	ss565764535	Apr 25, 2013 (138)
16	TISHKOFF	ss565764552	Apr 25, 2013 (138)
17	SSMP	ss664450849	Apr 01, 2015 (144)
18	BILGI_BIOE	ss666734687	Apr 25, 2013 (138)
19	EVA-GONL	ss994389180	Aug 21, 2014 (142)
20	1000GENOMES	ss1378240683	Aug 21, 2014 (142)
21	DDI	ss1536896252	Apr 01, 2015 (144)
22	EVA_GENOME_DK	ss1575307564	Apr 01, 2015 (144)
23	EVA_UK10K_ALSPAC	ss1709239680	Apr 01, 2015 (144)
24	EVA_UK10K_TWINSUK	ss1709239845	Apr 01, 2015 (144)
25	EVA_EXAC	ss1712211693	Apr 01, 2015 (144)
26	HAMMER_LAB	ss1809349856	Sep 08, 2015 (146)
27	GENOMED	ss1968658496	Jul 19, 2016 (147)
28	JJLAB	ss2031412164	Sep 14, 2016 (149)
29	ILLUMINA	ss2136295659	Dec 20, 2016 (150)
30	SYSTEMSBIOZJU	ss2629357112	Nov 08, 2017 (151)
31	GNOMAD	ss2744246415	Nov 08, 2017 (151)
32	GNOMAD	ss2750268421	Nov 08, 2017 (151)
33	GNOMAD	ss2963916432	Nov 08, 2017 (151)
34	SWEGEN	ss3017629701	Nov 08, 2017 (151)
35	ILLUMINA	ss3021919848	Nov 08, 2017 (151)
36	MCHAISSO	ss3063919912	Nov 08, 2017 (151)
37	MCHAISSO	ss3064768965	Nov 08, 2017 (151)
38	MCHAISSO	ss3065718789	Nov 08, 2017 (151)
39	BEROUKHIMLAB	ss3644439754	Oct 12, 2018 (152)
40	BIOINF_KMB_FNS_UNIBA	ss3645525787	Oct 12, 2018 (152)
41	URBANLAB	ss3650936352	Oct 12, 2018 (152)
42	ILLUMINA	ss3652346666	Oct 12, 2018 (152)
43	EVA_DECODE	ss3702950265	Jul 13, 2019 (153)
44	ILLUMINA	ss3725740331	Jul 13, 2019 (153)
45	ACPOP	ss3743117617	Jul 13, 2019 (153)
46	PACBIO	ss3788557125	Jul 13, 2019 (153)
47	PACBIO	ss3793462821	Jul 13, 2019 (153)
48	PACBIO	ss3798349740	Jul 13, 2019 (153)
49	KHV_HUMAN_GENOMES	ss3821419996	Jul 13, 2019 (153)
50	EVA	ss3825321180	Apr 27, 2020 (154)
51	EVA	ss3835508379	Apr 27, 2020 (154)
52	EVA	ss3841375804	Apr 27, 2020 (154)
53	EVA	ss3846882211	Apr 27, 2020 (154)
54	KOGIC	ss3981560280	Apr 27, 2020 (154)
55	FSA-LAB	ss3984161192	Apr 26, 2021 (155)
56	FSA-LAB	ss3984161193	Apr 26, 2021 (155)
57	EVA	ss3986081838	Apr 26, 2021 (155)
58	EVA	ss3986810641	Apr 26, 2021 (155)
59	TOPMED	ss5077807319	Apr 26, 2021 (155)
60	TOMMO_GENOMICS	ss5228203377	Apr 26, 2021 (155)
61	EVA	ss5236964891	Apr 26, 2021 (155)
62	EVA	ss5237248989	Apr 26, 2021 (155)
63	HUGCELL_USP	ss5500052105	Oct 13, 2022 (156)
64	1000G_HIGH_COVERAGE	ss5613454721	Oct 13, 2022 (156)
65	EVA	ss5623978991	Oct 13, 2022 (156)
66	EVA	ss5624093586	Oct 13, 2022 (156)
67	SANFORD_IMAGENETICS	ss5662578289	Oct 13, 2022 (156)
68	TOMMO_GENOMICS	ss5786988930	Oct 13, 2022 (156)
69	EVA	ss5800225460	Oct 13, 2022 (156)
70	YY_MCH	ss5817681035	Oct 13, 2022 (156)
71	EVA	ss5840678151	Oct 13, 2022 (156)
72	EVA	ss5848500640	Oct 13, 2022 (156)
73	EVA	ss5852322961	Oct 13, 2022 (156)
74	EVA	ss5928453250	Oct 13, 2022 (156)
75	EVA	ss5981063342	Oct 13, 2022 (156)
76	EVA	ss5981314163	Oct 13, 2022 (156)
77	1000Genomes	NC_000019.9 - 51835893	Oct 12, 2018 (152)
78	1000Genomes_30x	NC_000019.10 - 51332639	Oct 13, 2022 (156)
79	The Avon Longitudinal Study of Parents and Children	NC_000019.9 - 51835893	Oct 12, 2018 (152)
80	ExAC	NC_000019.9 - 51835893	Oct 12, 2018 (152)
81	The Danish reference pan genome	NC_000019.9 - 51835893	Apr 27, 2020 (154)
82	gnomAD - Genomes	NC_000019.10 - 51332639	Apr 26, 2021 (155)
83	gnomAD - Exomes	NC_000019.9 - 51835893	Jul 13, 2019 (153)
84	GO Exome Sequencing Project	NC_000019.9 - 51835893	Oct 12, 2018 (152)
85	Genome of the Netherlands Release 5	NC_000019.9 - 51835893	Apr 27, 2020 (154)
86	Korean Genome Project	NC_000019.10 - 51332639	Apr 27, 2020 (154)
87	Northern Sweden	NC_000019.9 - 51835893	Jul 13, 2019 (153)
88	8.3KJPN	NC_000019.9 - 51835893	Apr 26, 2021 (155)
89	14KJPN	NC_000019.10 - 51332639	Oct 13, 2022 (156)
90	TopMed	NC_000019.10 - 51332639	Apr 26, 2021 (155)
91	UK 10K study - Twins	NC_000019.9 - 51835893	Oct 12, 2018 (152)
92	ALFA	NC_000019.10 - 51332639	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)
rs11410501	May 15, 2013 (138)
rs33944140	May 23, 2006 (127)
rs35313368	May 11, 2012 (137)
rs58614229	May 25, 2008 (130)
rs138706482	Sep 17, 2011 (135)
rs141741623	Sep 17, 2011 (135)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss256208896, ss289393237, ss327913502, ss328038939, ss328280911, ss552633772, ss553023250, ss553667082	NC_000019.8:56527704::G	NC_000019.10:51332638:G:GG	(self)
ss294966582	NC_000019.8:56527705::G	NC_000019.10:51332638:G:GG	(self)
76944189, 42596679, 4278747, 639803, 13559730, 1778119, 18975379, 16402482, 86172684, 42596679, ss565764535, ss664450849, ss666734687, ss994389180, ss1378240683, ss1536896252, ss1575307564, ss1709239680, ss1709239845, ss1712211693, ss1809349856, ss1968658496, ss2031412164, ss2136295659, ss2629357112, ss2744246415, ss2750268421, ss2963916432, ss3017629701, ss3021919848, ss3644439754, ss3652346666, ss3743117617, ss3788557125, ss3793462821, ss3798349740, ss3825321180, ss3835508379, ss3841375804, ss3984161192, ss3986081838, ss3986810641, ss5228203377, ss5623978991, ss5624093586, ss5662578289, ss5800225460, ss5840678151, ss5981063342, ss5981314163	NC_000019.9:51835892::G	NC_000019.10:51332638:G:GG	(self)
ss565764552, ss3984161193, ss5848500640	NC_000019.9:51835893::G	NC_000019.10:51332638:G:GG	(self)
100980656, 542654008, 37938281, 120826034, 293352983, ss3063919912, ss3064768965, ss3065718789, ss3645525787, ss3650936352, ss3702950265, ss3725740331, ss3821419996, ss3846882211, ss3981560280, ss5077807319, ss5236964891, ss5237248989, ss5500052105, ss5613454721, ss5786988930, ss5817681035, ss5852322961, ss5928453250	NC_000019.10:51332638::G	NC_000019.10:51332638:G:GG	(self)
4722762520	NC_000019.10:51332638:G:GG	NC_000019.10:51332638:G:GG	(self)
ss288528043	NT_011109.16:24104110::G	NC_000019.10:51332638:G:GG	(self)
ss15286968, ss81110565, ss81127346, ss95731538	NT_011109.16:24104111::G	NC_000019.10:51332638:G:GG	(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 rs11402251

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

rs11402251