Name: rs62348766
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.

rs62348766

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:186211698 (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 / T>G
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.029793 (3966/133118, GnomAD)
T=0.10774 (8479/78698, PAGE_STUDY)
C=0.00237 (67/28258, 14KJPN) (+ 7 more)
T=0.25175 (5969/23710, ALFA)
C=0.00221 (37/16760, 8.3KJPN)
T=0.3942 (1155/2930, KOREAN)
C=0.0027 (5/1832, Korea1K)
T=0.384 (211/550, SGDP_PRJ)
T=0.398 (86/216, Qatari)
T=0.48 (25/52, Siberian)

Clinical Significance: Reported in ClinVar
Gene : Consequence: KLKB1 : 5 Prime UTR Variant
CYP4V2 : 3 Prime UTR 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	23710	T=0.25175	C=0.74825, G=0.00000
European	Sub	17638	T=0.24640	C=0.75360, G=0.00000
African	Sub	3008	T=0.2603	C=0.7397, G=0.0000
African Others	Sub	96	T=0.22	C=0.78, G=0.00
African American	Sub	2912	T=0.2617	C=0.7383, G=0.0000
Asian	Sub	158	T=0.203	C=0.797, G=0.000
East Asian	Sub	132	T=0.197	C=0.803, G=0.000
Other Asian	Sub	26	T=0.23	C=0.77, G=0.00
Latin American 1	Sub	168	T=0.321	C=0.679, G=0.000
Latin American 2	Sub	700	T=0.344	C=0.656, G=0.000
South Asian	Sub	116	T=0.353	C=0.647, G=0.000
Other	Sub	1922	T=0.2456	C=0.7544, G=0.0000

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
gnomAD - Genomes	Global	Study-wide	133118	T=0.970207	C=0.029793
gnomAD - Genomes	European	Sub	74630	T=0.99627	C=0.00373
gnomAD - Genomes	African	Sub	36660	T=0.90870	C=0.09130
gnomAD - Genomes	American	Sub	13352	T=0.98570	C=0.01430
gnomAD - Genomes	Ashkenazi Jewish	Sub	3294	T=0.9718	C=0.0282
gnomAD - Genomes	East Asian	Sub	3102	T=0.9990	C=0.0010
gnomAD - Genomes	Other	Sub	2080	T=0.9740	C=0.0260
The PAGE Study	Global	Study-wide	78698	T=0.10774	C=0.89226
The PAGE Study	AfricanAmerican	Sub	32514	T=0.11426	C=0.88574
The PAGE Study	Mexican	Sub	10810	T=0.11619	C=0.88381
The PAGE Study	Asian	Sub	8318	T=0.0708	C=0.9292
The PAGE Study	PuertoRican	Sub	7918	T=0.1181	C=0.8819
The PAGE Study	NativeHawaiian	Sub	4534	T=0.0644	C=0.9356
The PAGE Study	Cuban	Sub	4230	T=0.0979	C=0.9021
The PAGE Study	Dominican	Sub	3828	T=0.1019	C=0.8981
The PAGE Study	CentralAmerican	Sub	2450	T=0.1098	C=0.8902
The PAGE Study	SouthAmerican	Sub	1982	T=0.1731	C=0.8269
The PAGE Study	NativeAmerican	Sub	1260	T=0.1317	C=0.8683
The PAGE Study	SouthAsian	Sub	854	T=0.129	C=0.871
14KJPN	JAPANESE	Study-wide	28258	T=0.99763	C=0.00237
Allele Frequency Aggregator	Total	Global	23710	T=0.25175	C=0.74825, G=0.00000
Allele Frequency Aggregator	European	Sub	17638	T=0.24640	C=0.75360, G=0.00000
Allele Frequency Aggregator	African	Sub	3008	T=0.2603	C=0.7397, G=0.0000
Allele Frequency Aggregator	Other	Sub	1922	T=0.2456	C=0.7544, G=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	700	T=0.344	C=0.656, G=0.000
Allele Frequency Aggregator	Latin American 1	Sub	168	T=0.321	C=0.679, G=0.000
Allele Frequency Aggregator	Asian	Sub	158	T=0.203	C=0.797, G=0.000
Allele Frequency Aggregator	South Asian	Sub	116	T=0.353	C=0.647, G=0.000
8.3KJPN	JAPANESE	Study-wide	16760	T=0.99779	C=0.00221
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.3942	C=0.6058
Korean Genome Project	KOREAN	Study-wide	1832	T=0.9973	C=0.0027
SGDP_PRJ	Global	Study-wide	550	T=0.384	C=0.616
Qatari	Global	Study-wide	216	T=0.398	C=0.602
Siberian	Global	Study-wide	52	T=0.48	C=0.52

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.186211698T>C
GRCh38.p14 chr 4	NC_000004.12:g.186211698T>G
GRCh37.p13 chr 4	NC_000004.11:g.187132852T>C
GRCh37.p13 chr 4	NC_000004.11:g.187132852T>G
KLKB1 RefSeqGene (LRG_565)	NG_012095.2:g.7720T>C
KLKB1 RefSeqGene (LRG_565)	NG_012095.2:g.7720T>G
CYP4V2 RefSeqGene	NG_007965.1:g.25179T>C
CYP4V2 RefSeqGene	NG_007965.1:g.25179T>G

Gene: CYP4V2, cytochrome P450 family 4 subfamily V member 2 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CYP4V2 transcript	NM_207352.4:c.*1057=	N/A	3 Prime UTR Variant
CYP4V2 transcript variant X1	XM_005262935.5:c.*1057=	N/A	3 Prime UTR Variant
CYP4V2 transcript variant X2	XM_047450077.1:c.*1057=	N/A	3 Prime UTR Variant

Gene: KLKB1, kallikrein B1 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
KLKB1 transcript variant 1	NM_000892.5:c.	N/A	Genic Upstream Transcript Variant
KLKB1 transcript variant 2	NM_001318394.2:c.	N/A	Genic Upstream Transcript Variant
KLKB1 transcript variant 3	NM_001318396.2:c.	N/A	Genic Upstream Transcript Variant
KLKB1 transcript variant X3	XM_047415661.1:c.-3011=	N/A	5 Prime UTR Variant
KLKB1 transcript variant X1	XM_011531930.3:c.	N/A	Genic Upstream Transcript Variant
KLKB1 transcript variant X2	XM_017008181.2:c.	N/A	Genic Upstream Transcript Variant
KLKB1 transcript variant X4	XM_017008182.2:c.	N/A	Genic Upstream Transcript Variant
KLKB1 transcript variant X5	XM_017008183.2:c.	N/A	Genic Upstream Transcript Variant
KLKB1 transcript variant X6	XM_017008184.2:c.	N/A	Genic Upstream 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.

Allele: C (allele ID: 297956 )

ClinVar Accession	Disease Names	Clinical Significance
RCV000279040.3	Bietti crystalline corneoretinal dystrophy	Uncertain-Significance
RCV000380500.3	Corneal dystrophy	Uncertain-Significance

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	G
GRCh38.p14 chr 4	NC_000004.12:g.186211698=	NC_000004.12:g.186211698T>C	NC_000004.12:g.186211698T>G
GRCh37.p13 chr 4	NC_000004.11:g.187132852=	NC_000004.11:g.187132852T>C	NC_000004.11:g.187132852T>G
KLKB1 RefSeqGene (LRG_565)	NG_012095.2:g.7720=	NG_012095.2:g.7720T>C	NG_012095.2:g.7720T>G
CYP4V2 RefSeqGene	NG_007965.1:g.25179=	NG_007965.1:g.25179T>C	NG_007965.1:g.25179T>G
CYP4V2 transcript	NM_207352.4:c.*1057=	NM_207352.4:c.*1057T>C	NM_207352.4:c.*1057T>G
CYP4V2 transcript	NM_207352.3:c.*1057=	NM_207352.3:c.*1057T>C	NM_207352.3:c.*1057T>G
CYP4V2 transcript variant X1	XM_005262935.5:c.*1057=	XM_005262935.5:c.*1057T>C	XM_005262935.5:c.*1057T>G
CYP4V2 transcript variant X1	XM_005262935.4:c.*1057=	XM_005262935.4:c.*1057T>C	XM_005262935.4:c.*1057T>G
CYP4V2 transcript variant X1	XM_005262935.3:c.*1057=	XM_005262935.3:c.*1057T>C	XM_005262935.3:c.*1057T>G
CYP4V2 transcript variant X1	XM_005262935.2:c.*1057=	XM_005262935.2:c.*1057T>C	XM_005262935.2:c.*1057T>G
CYP4V2 transcript variant X1	XM_005262935.1:c.*1057=	XM_005262935.1:c.*1057T>C	XM_005262935.1:c.*1057T>G
KLKB1 transcript variant X3	XM_047415661.1:c.-3011=	XM_047415661.1:c.-3011T>C	XM_047415661.1:c.-3011T>G
CYP4V2 transcript variant X2	XM_047450077.1:c.*1057=	XM_047450077.1:c.*1057T>C	XM_047450077.1:c.*1057T>G

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#.

43 SubSNP, 10 Frequency, 2 ClinVar submissions

No	Submitter	Submission ID	Date (Build)
1	BCMHGSC_JDW	ss92933408	Mar 24, 2008 (129)
2	HUMANGENOME_JCVI	ss98899680	Feb 03, 2009 (144)
3	ILLUMINA-UK	ss117340435	Dec 01, 2009 (131)
4	ENSEMBL	ss142681008	Dec 01, 2009 (131)
5	GMI	ss154789394	Dec 01, 2009 (131)
6	COMPLETE_GENOMICS	ss167515137	Jul 04, 2010 (132)
7	BUSHMAN	ss199685447	Jul 04, 2010 (132)
8	BCM-HGSC-SUB	ss206662621	Jul 04, 2010 (132)
9	BL	ss253834825	May 09, 2011 (134)
10	GMI	ss278102083	May 04, 2012 (137)
11	GMI	ss285087391	Apr 25, 2013 (138)
12	ILLUMINA	ss484180657	May 04, 2012 (137)
13	ILLUMINA	ss484777537	May 04, 2012 (137)
14	ILLUMINA	ss536369139	Sep 08, 2015 (146)
15	ILLUMINA	ss779527733	Sep 08, 2015 (146)
16	ILLUMINA	ss782536239	Sep 08, 2015 (146)
17	ILLUMINA	ss834998269	Sep 08, 2015 (146)
18	HAMMER_LAB	ss1802796368	Sep 08, 2015 (146)
19	WEILL_CORNELL_DGM	ss1924363227	Feb 12, 2016 (147)
20	ILLUMINA	ss1958750700	Feb 12, 2016 (147)
21	USC_VALOUEV	ss2150911568	Dec 20, 2016 (150)
22	ILLUMINA	ss2634227734	Nov 08, 2017 (151)
23	GRF	ss2706420651	Nov 08, 2017 (151)
24	SWEGEN	ss2996218548	Nov 08, 2017 (151)
25	ILLUMINA	ss3022449761	Nov 08, 2017 (151)
26	CSHL	ss3346163691	Nov 08, 2017 (151)
27	ILLUMINA	ss3629149409	Oct 12, 2018 (152)
28	ILLUMINA	ss3632157862	Oct 12, 2018 (152)
29	URBANLAB	ss3647950756	Oct 12, 2018 (152)
30	ILLUMINA	ss3652941392	Oct 12, 2018 (152)
31	EVA_DECODE	ss3713864231	Jul 13, 2019 (153)
32	ILLUMINA	ss3726202042	Jul 13, 2019 (153)
33	PAGE_CC	ss3771177625	Jul 13, 2019 (153)
34	SGDP_PRJ	ss3860919506	Apr 26, 2020 (154)
35	KRGDB	ss3907306670	Apr 26, 2020 (154)
36	KOGIC	ss3955879062	Apr 26, 2020 (154)
37	GNOMAD	ss4097368948	Apr 26, 2021 (155)
38	TOMMO_GENOMICS	ss5169822103	Apr 26, 2021 (155)
39	1000G_HIGH_COVERAGE	ss5262447419	Oct 13, 2022 (156)
40	EVA	ss5315021037	Oct 13, 2022 (156)
41	HUGCELL_USP	ss5460853433	Oct 13, 2022 (156)
42	TOMMO_GENOMICS	ss5705313470	Oct 13, 2022 (156)
43	EVA	ss5980270237	Oct 13, 2022 (156)
44	gnomAD - Genomes	NC_000004.12 - 186211698	Apr 26, 2021 (155)
45	KOREAN population from KRGDB	NC_000004.11 - 187132852	Apr 26, 2020 (154)
46	Korean Genome Project	NC_000004.12 - 186211698	Apr 26, 2020 (154)
47	The PAGE Study	NC_000004.12 - 186211698	Jul 13, 2019 (153)
48	Qatari	NC_000004.11 - 187132852	Apr 26, 2020 (154)
49	SGDP_PRJ	NC_000004.11 - 187132852	Apr 26, 2020 (154)
50	Siberian	NC_000004.11 - 187132852	Apr 26, 2020 (154)
51	8.3KJPN	NC_000004.11 - 187132852	Apr 26, 2021 (155)
52	14KJPN	NC_000004.12 - 186211698	Oct 13, 2022 (156)
53	ALFA	NC_000004.12 - 186211698	Apr 26, 2021 (155)
54	ClinVar	RCV000279040.3	Oct 13, 2022 (156)
55	ClinVar	RCV000380500.3	Oct 13, 2022 (156)

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)
rs66511256	Jul 02, 2015 (144)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss92933408, ss117340435, ss167515137, ss199685447, ss206662621, ss253834825, ss278102083, ss285087391, ss484777537	NC_000004.10:187369845:T:C	NC_000004.12:186211697:T:C	(self)
14484064, 6405157, 12936486, 3427922, 27791410, ss484180657, ss536369139, ss779527733, ss782536239, ss834998269, ss1802796368, ss1924363227, ss1958750700, ss2150911568, ss2634227734, ss2706420651, ss2996218548, ss3022449761, ss3346163691, ss3629149409, ss3632157862, ss3652941392, ss3860919506, ss3907306670, ss5169822103, ss5315021037, ss5980270237	NC_000004.11:187132851:T:C	NC_000004.12:186211697:T:C	(self)
RCV000279040.3, RCV000380500.3, 176638962, 12257063, 399094, 39150574, 8050835410, ss3647950756, ss3713864231, ss3726202042, ss3771177625, ss3955879062, ss4097368948, ss5262447419, ss5460853433, ss5705313470	NC_000004.12:186211697:T:C	NC_000004.12:186211697:T:C	(self)
ss98899680, ss142681008, ss154789394	NT_016354.19:111680572:T:C	NC_000004.12:186211697:T:C	(self)
8050835410	NC_000004.12:186211697:T:G	NC_000004.12:186211697:T:G	(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 rs62348766

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

rs62348766