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dbSNP Short Genetic Variations

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.

rs587779411

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr8:1780498 (GRCh38.p13) 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>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000004 (1/251310, GnomAD_exome)
G=0.000007 (1/140286, GnomAD)
G=0.000008 (1/121178, ExAC) (+ 2 more)
G=0.00000 (0/78696, PAGE_STUDY)
G=0.00000 (0/10680, ALFA)
Clinical Significance
Reported in ClinVar
Gene : Consequence
CLN8 : Missense Variant
Publications
1 citation
Genomic View
See rs on genome
Help

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.p13 chr 8 NC_000008.11:g.1780498C>G
GRCh38.p13 chr 8 NC_000008.11:g.1780498C>T
GRCh37.p13 chr 8 NC_000008.10:g.1728664C>G
GRCh37.p13 chr 8 NC_000008.10:g.1728664C>T
CLN8 RefSeqGene (LRG_691) NG_008656.2:g.29721C>G
CLN8 RefSeqGene (LRG_691) NG_008656.2:g.29721C>T
GRCh38.p13 chr 8 alt locus HSCHR8_7_CTG1 NT_187680.1:g.193156C>G
GRCh38.p13 chr 8 alt locus HSCHR8_7_CTG1 NT_187680.1:g.193156C>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.792C>G N [AAC] > K [AAG] Coding Sequence Variant
protein CLN8 NP_061764.2:p.Asn264Lys N (Asn) > K (Lys) Missense Variant
CLN8 transcript NM_018941.4:c.792C>T N [AAC] > N [AAT] Coding Sequence Variant
protein CLN8 NP_061764.2:p.Asn264= N (Asn) > N (Asn) Synonymous Variant
CLN8 transcript variant X6 XM_011534747.2:c. N/A Genic Downstream Transcript Variant
CLN8 transcript variant X3 XM_005266022.1:c.792C>G N [AAC] > K [AAG] Coding Sequence Variant
protein CLN8 isoform X1 XP_005266079.1:p.Asn264Lys N (Asn) > K (Lys) Missense Variant
CLN8 transcript variant X3 XM_005266022.1:c.792C>T N [AAC] > N [AAT] Coding Sequence Variant
protein CLN8 isoform X1 XP_005266079.1:p.Asn264= N (Asn) > N (Asn) Synonymous Variant
CLN8 transcript variant X5 XM_005266023.1:c.792C>G N [AAC] > K [AAG] Coding Sequence Variant
protein CLN8 isoform X1 XP_005266080.1:p.Asn264Lys N (Asn) > K (Lys) Missense Variant
CLN8 transcript variant X5 XM_005266023.1:c.792C>T N [AAC] > N [AAT] Coding Sequence Variant
protein CLN8 isoform X1 XP_005266080.1:p.Asn264= N (Asn) > N (Asn) Synonymous Variant
CLN8 transcript variant X2 XM_011534745.1:c.792C>G N [AAC] > K [AAG] Coding Sequence Variant
protein CLN8 isoform X1 XP_011533047.1:p.Asn264Lys N (Asn) > K (Lys) Missense Variant
CLN8 transcript variant X2 XM_011534745.1:c.792C>T N [AAC] > N [AAT] Coding Sequence Variant
protein CLN8 isoform X1 XP_011533047.1:p.Asn264= N (Asn) > N (Asn) Synonymous Variant
CLN8 transcript variant X4 XM_011534746.2:c.792C>G N [AAC] > K [AAG] Coding Sequence Variant
protein CLN8 isoform X1 XP_011533048.1:p.Asn264Lys N (Asn) > K (Lys) Missense Variant
CLN8 transcript variant X4 XM_011534746.2:c.792C>T N [AAC] > N [AAT] Coding Sequence Variant
protein CLN8 isoform X1 XP_011533048.1:p.Asn264= N (Asn) > N (Asn) Synonymous Variant
CLN8 transcript variant X1 XM_005266021.4:c.792C>G N [AAC] > K [AAG] Coding Sequence Variant
protein CLN8 isoform X1 XP_005266078.1:p.Asn264Lys N (Asn) > K (Lys) Missense Variant
CLN8 transcript variant X1 XM_005266021.4:c.792C>T N [AAC] > N [AAT] Coding Sequence Variant
protein CLN8 isoform X1 XP_005266078.1:p.Asn264= N (Asn) > N (Asn) Synonymous Variant
Help

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: G (allele ID: 106601 )
ClinVar Accession Disease Names Clinical Significance
RCV000087102.1 Neuronal ceroid lipofuscinosis 8 Pathogenic
RCV000201947.1 Neuronal ceroid lipofuscinosis 8 Likely-Pathogenic
RCV000988030.1 Neuronal ceroid lipofuscinosis Likely-Pathogenic

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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 10680 C=1.00000 G=0.00000
European Sub 6962 C=1.0000 G=0.0000
African Sub 2294 C=1.0000 G=0.0000
African Others Sub 84 C=1.00 G=0.00
African American Sub 2210 C=1.0000 G=0.0000
Asian Sub 108 C=1.000 G=0.000
East Asian Sub 84 C=1.00 G=0.00
Other Asian Sub 24 C=1.00 G=0.00
Latin American 1 Sub 146 C=1.000 G=0.000
Latin American 2 Sub 610 C=1.000 G=0.000
South Asian Sub 94 C=1.00 G=0.00
Other Sub 466 C=1.000 G=0.000


Help

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").

Download
Study Population Group Sample Size Ref Allele Alt Allele
gnomAD - Exomes Global Study-wide 251310 C=0.999996 T=0.000004
gnomAD - Exomes European Sub 135260 C=1.000000 T=0.000000
gnomAD - Exomes Asian Sub 49008 C=0.99998 T=0.00002
gnomAD - Exomes American Sub 34582 C=1.00000 T=0.00000
gnomAD - Exomes African Sub 16248 C=1.00000 T=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10076 C=1.00000 T=0.00000
gnomAD - Exomes Other Sub 6136 C=1.0000 T=0.0000
gnomAD - Genomes Global Study-wide 140286 C=0.999993 G=0.000007
gnomAD - Genomes European Sub 75956 C=0.99999 G=0.00001
gnomAD - Genomes African Sub 42062 C=1.00000 G=0.00000
gnomAD - Genomes American Sub 13660 C=1.00000 G=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3322 C=1.0000 G=0.0000
gnomAD - Genomes East Asian Sub 3134 C=1.0000 G=0.0000
gnomAD - Genomes Other Sub 2152 C=1.0000 G=0.0000
ExAC Global Study-wide 121178 C=0.999992 G=0.000008
ExAC Europe Sub 73226 C=0.99999 G=0.00001
ExAC Asian Sub 25144 C=1.00000 G=0.00000
ExAC American Sub 11566 C=1.00000 G=0.00000
ExAC African Sub 10336 C=1.00000 G=0.00000
ExAC Other Sub 906 C=1.000 G=0.000
The PAGE Study Global Study-wide 78696 C=1.00000 G=0.00000
The PAGE Study AfricanAmerican Sub 32510 C=1.00000 G=0.00000
The PAGE Study Mexican Sub 10810 C=1.00000 G=0.00000
The PAGE Study Asian Sub 8318 C=1.0000 G=0.0000
The PAGE Study PuertoRican Sub 7918 C=1.0000 G=0.0000
The PAGE Study NativeHawaiian Sub 4534 C=1.0000 G=0.0000
The PAGE Study Cuban Sub 4230 C=1.0000 G=0.0000
The PAGE Study Dominican Sub 3828 C=1.0000 G=0.0000
The PAGE Study CentralAmerican Sub 2450 C=1.0000 G=0.0000
The PAGE Study SouthAmerican Sub 1982 C=1.0000 G=0.0000
The PAGE Study NativeAmerican Sub 1260 C=1.0000 G=0.0000
The PAGE Study SouthAsian Sub 856 C=1.000 G=0.000
Help

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= G T
GRCh38.p13 chr 8 NC_000008.11:g.1780498= NC_000008.11:g.1780498C>G NC_000008.11:g.1780498C>T
GRCh37.p13 chr 8 NC_000008.10:g.1728664= NC_000008.10:g.1728664C>G NC_000008.10:g.1728664C>T
CLN8 RefSeqGene (LRG_691) NG_008656.2:g.29721= NG_008656.2:g.29721C>G NG_008656.2:g.29721C>T
CLN8 transcript NM_018941.4:c.792= NM_018941.4:c.792C>G NM_018941.4:c.792C>T
CLN8 transcript NM_018941.3:c.792= NM_018941.3:c.792C>G NM_018941.3:c.792C>T
GRCh38.p13 chr 8 alt locus HSCHR8_7_CTG1 NT_187680.1:g.193156= NT_187680.1:g.193156C>G NT_187680.1:g.193156C>T
CLN8 transcript variant X1 XM_005266021.4:c.792= XM_005266021.4:c.792C>G XM_005266021.4:c.792C>T
CLN8 transcript variant X1 XM_005266021.1:c.792= XM_005266021.1:c.792C>G XM_005266021.1:c.792C>T
CLN8 transcript variant X4 XM_011534746.2:c.792= XM_011534746.2:c.792C>G XM_011534746.2:c.792C>T
CLN8 transcript variant X3 XM_005266022.1:c.792= XM_005266022.1:c.792C>G XM_005266022.1:c.792C>T
CLN8 transcript variant X2 XM_011534745.1:c.792= XM_011534745.1:c.792C>G XM_011534745.1:c.792C>T
CLN8 transcript variant X5 XM_005266023.1:c.792= XM_005266023.1:c.792C>G XM_005266023.1:c.792C>T
protein CLN8 NP_061764.2:p.Asn264= NP_061764.2:p.Asn264Lys NP_061764.2:p.Asn264=
protein CLN8 isoform X1 XP_005266078.1:p.Asn264= XP_005266078.1:p.Asn264Lys XP_005266078.1:p.Asn264=
protein CLN8 isoform X1 XP_011533048.1:p.Asn264= XP_011533048.1:p.Asn264Lys XP_011533048.1:p.Asn264=
protein CLN8 isoform X1 XP_005266079.1:p.Asn264= XP_005266079.1:p.Asn264Lys XP_005266079.1:p.Asn264=
protein CLN8 isoform X1 XP_011533047.1:p.Asn264= XP_011533047.1:p.Asn264Lys XP_011533047.1:p.Asn264=
protein CLN8 isoform X1 XP_005266080.1:p.Asn264= XP_005266080.1:p.Asn264Lys XP_005266080.1:p.Asn264=
Help

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#.

11 SubSNP, 5 Frequency, 3 ClinVar submissions
No Submitter Submission ID Date (Build)
1 CLINVAR ss1457611841 Nov 23, 2014 (142)
2 EVA_EXAC ss1689058342 Apr 01, 2015 (144)
3 ILLUMINA ss1959075811 Feb 12, 2016 (147)
4 HUMAN_LONGEVITY ss2299716740 Dec 20, 2016 (150)
5 GNOMAD ss2736942690 Nov 08, 2017 (151)
6 GNOMAD ss2747980028 Nov 08, 2017 (151)
7 GNOMAD ss2861831160 Nov 08, 2017 (151)
8 ILLUMINA ss3022806142 Nov 08, 2017 (151)
9 ILLUMINA ss3653342843 Oct 12, 2018 (152)
10 ILLUMINA ss3726503582 Jul 13, 2019 (153)
11 PAGE_CC ss3771415475 Jul 13, 2019 (153)
12 ExAC NC_000008.10 - 1728664 Oct 12, 2018 (152)
13 gnomAD - Genomes NC_000008.11 - 1780498 Apr 26, 2021 (155)
14 gnomAD - Exomes NC_000008.10 - 1728664 Jul 13, 2019 (153)
15 The PAGE Study NC_000008.11 - 1780498 Jul 13, 2019 (153)
16 ALFA NC_000008.11 - 1780498 Apr 26, 2021 (155)
17 ClinVar RCV000087102.1 Oct 12, 2018 (152)
18 ClinVar RCV000201947.1 Oct 12, 2018 (152)
19 ClinVar RCV000988030.1 Apr 26, 2020 (154)
Help

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
9148862, ss1689058342, ss1959075811, ss2747980028, ss2861831160, ss3022806142, ss3653342843 NC_000008.10:1728663:C:G NC_000008.11:1780497:C:G (self)
RCV000087102.1, RCV000201947.1, RCV000988030.1, 283522428, 636944, 14076968692, ss1457611841, ss2299716740, ss3726503582, ss3771415475 NC_000008.11:1780497:C:G NC_000008.11:1780497:C:G (self)
6106179, ss2736942690 NC_000008.10:1728663:C:T NC_000008.11:1780497:C:T (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

1 citation for rs587779411
PMID Title Author Year Journal
16570191 Novel mutations in CLN8 in Italian variant late infantile neuronal ceroid lipofuscinosis: Another genetic hit in the Mediterranean. Cannelli N et al. 2006 Neurogenetics
Help

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.

Software version is: 2.0.1.post596+ae089ad