Name: rs62476924
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.

rs62476924

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr8:1782185 (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>T
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.15960 (4510/28258, 14KJPN)
A=0.02499 (426/17048, ALFA)
A=0.15973 (2677/16760, 8.3KJPN) (+ 14 more)
A=0.0874 (560/6404, 1000G_30x)
A=0.0925 (463/5008, 1000G)
A=0.0902 (404/4480, Estonian)
A=0.0807 (311/3854, ALSPAC)
A=0.0925 (343/3708, TWINSUK)
A=0.1314 (385/2930, KOREAN)
A=0.096 (96/998, GoNL)
A=0.100 (60/600, NorthernSweden)
A=0.056 (12/216, Qatari)
A=0.126 (27/214, Vietnamese)
C=0.442 (53/120, SGDP_PRJ)
A=0.12 (5/40, GENOME_DK)
C=0.50 (6/12, Siberian)
A=0.50 (6/12, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: CLN8 : 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	17048	C=0.97501	A=0.02499, T=0.00000
European	Sub	12734	C=0.96733	A=0.03267, T=0.00000
African	Sub	2834	C=0.9989	A=0.0011, T=0.0000
African Others	Sub	114	C=1.000	A=0.000, T=0.000
African American	Sub	2720	C=0.9989	A=0.0011, T=0.0000
Asian	Sub	92	C=1.00	A=0.00, T=0.00
East Asian	Sub	74	C=1.00	A=0.00, T=0.00
Other Asian	Sub	18	C=1.00	A=0.00, T=0.00
Latin American 1	Sub	134	C=1.000	A=0.000, T=0.000
Latin American 2	Sub	572	C=1.000	A=0.000, T=0.000
South Asian	Sub	56	C=1.00	A=0.00, T=0.00
Other	Sub	626	C=0.989	A=0.011, T=0.000

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
14KJPN	JAPANESE	Study-wide	28258	C=0.84040	A=0.15960
Allele Frequency Aggregator	Total	Global	17048	C=0.97501	A=0.02499, T=0.00000
Allele Frequency Aggregator	European	Sub	12734	C=0.96733	A=0.03267, T=0.00000
Allele Frequency Aggregator	African	Sub	2834	C=0.9989	A=0.0011, T=0.0000
Allele Frequency Aggregator	Other	Sub	626	C=0.989	A=0.011, T=0.000
Allele Frequency Aggregator	Latin American 2	Sub	572	C=1.000	A=0.000, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	134	C=1.000	A=0.000, T=0.000
Allele Frequency Aggregator	Asian	Sub	92	C=1.00	A=0.00, T=0.00
Allele Frequency Aggregator	South Asian	Sub	56	C=1.00	A=0.00, T=0.00
8.3KJPN	JAPANESE	Study-wide	16760	C=0.84027	A=0.15973
1000Genomes_30x	Global	Study-wide	6404	C=0.9126	A=0.0874
1000Genomes_30x	African	Sub	1786	C=0.9922	A=0.0078
1000Genomes_30x	Europe	Sub	1266	C=0.9179	A=0.0821
1000Genomes_30x	South Asian	Sub	1202	C=0.7953	A=0.2047
1000Genomes_30x	East Asian	Sub	1170	C=0.8598	A=0.1402
1000Genomes_30x	American	Sub	980	C=0.967	A=0.033
1000Genomes	Global	Study-wide	5008	C=0.9075	A=0.0925
1000Genomes	African	Sub	1322	C=0.9917	A=0.0083
1000Genomes	East Asian	Sub	1008	C=0.8562	A=0.1438
1000Genomes	Europe	Sub	1006	C=0.9195	A=0.0805
1000Genomes	South Asian	Sub	978	C=0.794	A=0.206
1000Genomes	American	Sub	694	C=0.964	A=0.036
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.9098	A=0.0902
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.9193	A=0.0807
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.9075	A=0.0925
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.8686	A=0.1314
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.904	A=0.096
Northern Sweden	ACPOP	Study-wide	600	C=0.900	A=0.100
Qatari	Global	Study-wide	216	C=0.944	A=0.056
A Vietnamese Genetic Variation Database	Global	Study-wide	214	C=0.874	A=0.126
SGDP_PRJ	Global	Study-wide	120	C=0.442	A=0.558
The Danish reference pan genome	Danish	Study-wide	40	C=0.88	A=0.12
Siberian	Global	Study-wide	12	C=0.50	A=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 8	NC_000008.11:g.1782185C>A
GRCh38.p14 chr 8	NC_000008.11:g.1782185C>T
GRCh37.p13 chr 8	NC_000008.10:g.1730351C>A
GRCh37.p13 chr 8	NC_000008.10:g.1730351C>T
CLN8 RefSeqGene (LRG_691)	NG_008656.2:g.31408C>A
CLN8 RefSeqGene (LRG_691)	NG_008656.2:g.31408C>T
GRCh38.p14 chr 8 alt locus HSCHR8_7_CTG1	NT_187680.1:g.194843C>A
GRCh38.p14 chr 8 alt locus HSCHR8_7_CTG1	NT_187680.1:g.194843C>T

Gene: CLN8, CLN8 transmembrane ER and ERGIC protein (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CLN8 transcript	NM_018941.4:c.*1618=	N/A	3 Prime UTR Variant
CLN8 transcript variant X1	XM_005266021.5:c.*1618=	N/A	3 Prime UTR Variant
CLN8 transcript variant X2	XM_005266022.2:c.*1618=	N/A	3 Prime UTR Variant
CLN8 transcript variant X3	XM_011534745.2:c.*1618=	N/A	3 Prime UTR Variant
CLN8 transcript variant X4	XM_011534746.3:c.*1618=	N/A	3 Prime UTR Variant
CLN8 transcript variant X5	XM_005266023.2:c.*1618=	N/A	3 Prime UTR Variant
CLN8 transcript variant X6	XM_047421512.1:c.*1618=	N/A	3 Prime UTR Variant
CLN8 transcript variant X7	XM_011534747.3:c.	N/A	Genic Downstream Transcript Variant
CLN8 transcript variant X8	XM_047421513.1:c.	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	T
GRCh38.p14 chr 8	NC_000008.11:g.1782185=	NC_000008.11:g.1782185C>A	NC_000008.11:g.1782185C>T
GRCh37.p13 chr 8	NC_000008.10:g.1730351=	NC_000008.10:g.1730351C>A	NC_000008.10:g.1730351C>T
CLN8 RefSeqGene (LRG_691)	NG_008656.2:g.31408=	NG_008656.2:g.31408C>A	NG_008656.2:g.31408C>T
CLN8 transcript	NM_018941.4:c.*1618=	NM_018941.4:c.*1618C>A	NM_018941.4:c.*1618C>T
CLN8 transcript	NM_018941.3:c.*1618=	NM_018941.3:c.*1618C>A	NM_018941.3:c.*1618C>T
GRCh38.p14 chr 8 alt locus HSCHR8_7_CTG1	NT_187680.1:g.194843=	NT_187680.1:g.194843C>A	NT_187680.1:g.194843C>T
CLN8 transcript variant X1	XM_005266021.5:c.*1618=	XM_005266021.5:c.*1618C>A	XM_005266021.5:c.*1618C>T
CLN8 transcript variant X4	XM_011534746.3:c.*1618=	XM_011534746.3:c.*1618C>A	XM_011534746.3:c.*1618C>T
CLN8 transcript variant X2	XM_005266022.2:c.*1618=	XM_005266022.2:c.*1618C>A	XM_005266022.2:c.*1618C>T
CLN8 transcript variant X3	XM_011534745.2:c.*1618=	XM_011534745.2:c.*1618C>A	XM_011534745.2:c.*1618C>T
CLN8 transcript variant X5	XM_005266023.2:c.*1618=	XM_005266023.2:c.*1618C>A	XM_005266023.2:c.*1618C>T
CLN8 transcript variant X6	XM_047421512.1:c.*1618=	XM_047421512.1:c.*1618C>A	XM_047421512.1:c.*1618C>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#.

49 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	BCMHGSC_JDW	ss93809268	Mar 25, 2008 (129)
2	ENSEMBL	ss143161404	Dec 01, 2009 (131)
3	GMI	ss155836141	Dec 01, 2009 (131)
4	COMPLETE_GENOMICS	ss162017022	Jul 04, 2010 (132)
5	1000GENOMES	ss234262539	Jul 15, 2010 (132)
6	1000GENOMES	ss241155574	Jul 15, 2010 (132)
7	GMI	ss279630429	May 04, 2012 (137)
8	SSMP	ss654883125	Apr 25, 2013 (138)
9	EVA-GONL	ss985052887	Aug 21, 2014 (142)
10	JMKIDD_LAB	ss1075166959	Aug 21, 2014 (142)
11	1000GENOMES	ss1328093751	Aug 21, 2014 (142)
12	DDI	ss1431362532	Apr 01, 2015 (144)
13	EVA_GENOME_DK	ss1582498714	Apr 01, 2015 (144)
14	EVA_DECODE	ss1594639561	Apr 01, 2015 (144)
15	EVA_UK10K_ALSPAC	ss1619707585	Apr 01, 2015 (144)
16	EVA_UK10K_TWINSUK	ss1662701618	Apr 01, 2015 (144)
17	WEILL_CORNELL_DGM	ss1928328009	Feb 12, 2016 (147)
18	JJLAB	ss2024850482	Sep 14, 2016 (149)
19	USC_VALOUEV	ss2153080518	Dec 20, 2016 (150)
20	HUMAN_LONGEVITY	ss2299716883	Dec 20, 2016 (150)
21	GRF	ss2708821772	Nov 08, 2017 (151)
22	GNOMAD	ss2861831358	Nov 08, 2017 (151)
23	SWEGEN	ss3002448827	Nov 08, 2017 (151)
24	BIOINF_KMB_FNS_UNIBA	ss3026214337	Nov 08, 2017 (151)
25	CSHL	ss3347970306	Nov 08, 2017 (151)
26	EGCUT_WGS	ss3670164039	Jul 13, 2019 (153)
27	EVA_DECODE	ss3721169075	Jul 13, 2019 (153)
28	ACPOP	ss3735283331	Jul 13, 2019 (153)
29	EVA	ss3767457266	Jul 13, 2019 (153)
30	KHV_HUMAN_GENOMES	ss3810624198	Jul 13, 2019 (153)
31	EVA	ss3830942350	Apr 26, 2020 (154)
32	SGDP_PRJ	ss3868950843	Apr 26, 2020 (154)
33	KRGDB	ss3916369788	Apr 26, 2020 (154)
34	VINODS	ss4027085225	Apr 26, 2021 (155)
35	TOPMED	ss4771709111	Apr 26, 2021 (155)
36	TOPMED	ss4771709112	Apr 26, 2021 (155)
37	TOMMO_GENOMICS	ss5186715615	Apr 26, 2021 (155)
38	1000G_HIGH_COVERAGE	ss5275613220	Oct 14, 2022 (156)
39	EVA	ss5378338493	Oct 14, 2022 (156)
40	HUGCELL_USP	ss5472364790	Oct 14, 2022 (156)
41	EVA	ss5509207218	Oct 14, 2022 (156)
42	1000G_HIGH_COVERAGE	ss5565166500	Oct 14, 2022 (156)
43	SANFORD_IMAGENETICS	ss5644488867	Oct 14, 2022 (156)
44	TOMMO_GENOMICS	ss5728079272	Oct 14, 2022 (156)
45	YY_MCH	ss5809319420	Oct 14, 2022 (156)
46	EVA	ss5829939978	Oct 14, 2022 (156)
47	EVA	ss5856195983	Oct 14, 2022 (156)
48	EVA	ss5887238320	Oct 14, 2022 (156)
49	EVA	ss5973682265	Oct 14, 2022 (156)
50	1000Genomes	NC_000008.10 - 1730351	Oct 12, 2018 (152)
51	1000Genomes_30x	NC_000008.11 - 1782185	Oct 14, 2022 (156)
52	The Avon Longitudinal Study of Parents and Children	NC_000008.10 - 1730351	Oct 12, 2018 (152)
53	Genetic variation in the Estonian population	NC_000008.10 - 1730351	Oct 12, 2018 (152)
54	The Danish reference pan genome	NC_000008.10 - 1730351	Apr 26, 2020 (154)
55	gnomAD - Genomes Submission ignored due to conflicting rows: Row 283522964 (NC_000008.11:1782184:C:A 9289/140044) Row 283522965 (NC_000008.11:1782184:C:T 2/140064)	-	Apr 26, 2021 (155)
56	gnomAD - Genomes Submission ignored due to conflicting rows: Row 283522964 (NC_000008.11:1782184:C:A 9289/140044) Row 283522965 (NC_000008.11:1782184:C:T 2/140064)	-	Apr 26, 2021 (155)
57	Genome of the Netherlands Release 5	NC_000008.10 - 1730351	Apr 26, 2020 (154)
58	KOREAN population from KRGDB	NC_000008.10 - 1730351	Apr 26, 2020 (154)
59	Northern Sweden	NC_000008.10 - 1730351	Jul 13, 2019 (153)
60	Qatari	NC_000008.10 - 1730351	Apr 26, 2020 (154)
61	SGDP_PRJ	NC_000008.10 - 1730351	Apr 26, 2020 (154)
62	Siberian	NC_000008.10 - 1730351	Apr 26, 2020 (154)
63	8.3KJPN	NC_000008.10 - 1730351	Apr 26, 2021 (155)
64	14KJPN	NC_000008.11 - 1782185	Oct 14, 2022 (156)
65	TopMed Submission ignored due to conflicting rows: Row 609086671 (NC_000008.11:1782184:C:A 16007/264690) Row 609086672 (NC_000008.11:1782184:C:T 5/264690)	-	Apr 26, 2021 (155)
66	TopMed Submission ignored due to conflicting rows: Row 609086671 (NC_000008.11:1782184:C:A 16007/264690) Row 609086672 (NC_000008.11:1782184:C:T 5/264690)	-	Apr 26, 2021 (155)
67	UK 10K study - Twins	NC_000008.10 - 1730351	Oct 12, 2018 (152)
68	A Vietnamese Genetic Variation Database	NC_000008.10 - 1730351	Jul 13, 2019 (153)
69	ALFA	NC_000008.11 - 1782185	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
ss93809268, ss162017022, ss279630429, ss1594639561	NC_000008.9:1717757:C:A	NC_000008.11:1782184:C:A	(self)
40171280, 22341590, 15902287, 8663652, 9973448, 23547182, 8568196, 10369939, 20967823, 5596872, 44684922, 22341590, 4973427, ss234262539, ss241155574, ss654883125, ss985052887, ss1075166959, ss1328093751, ss1431362532, ss1582498714, ss1619707585, ss1662701618, ss1928328009, ss2024850482, ss2153080518, ss2708821772, ss2861831358, ss3002448827, ss3347970306, ss3670164039, ss3735283331, ss3767457266, ss3830942350, ss3868950843, ss3916369788, ss5186715615, ss5378338493, ss5509207218, ss5644488867, ss5829939978, ss5973682265	NC_000008.10:1730350:C:A	NC_000008.11:1782184:C:A	(self)
52692435, 61916376, 3603177296, ss2299716883, ss3026214337, ss3721169075, ss3810624198, ss4771709111, ss5275613220, ss5472364790, ss5565166500, ss5728079272, ss5809319420, ss5856195983, ss5887238320	NC_000008.11:1782184:C:A	NC_000008.11:1782184:C:A	(self)
ss143161404, ss155836141	NT_023736.17:1720350:C:A	NC_000008.11:1782184:C:A	(self)
ss4027085225	NT_187680.1:194842:C:A	NC_000008.11:1782184:C:A	(self)
3603177296, ss4771709112	NC_000008.11:1782184:C:T	NC_000008.11:1782184: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 rs62476924

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

rs62476924