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dbSNP Short Genetic Variations

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.

rs121909098

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr18:57661207 (GRCh38.p12) 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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.00002 (4/246104, GnomAD)
T=0.00002 (2/125568, TOPMED)
T=0.00002 (2/121154, ExAC) (+ 1 more)
T=0.0000 (1/30960, GnomAD)
Clinical Significance
Reported in ClinVar
Gene : Consequence
ATP8B1 : Missense Variant
LOC100505549 : Intron 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.p12 chr 18 NC_000018.10:g.57661207C>T
GRCh37.p13 chr 18 NC_000018.9:g.55328439C>T
ATP8B1 RefSeqGene NG_007148.2:g.146889G>A
Gene: LOC100505549, uncharacterized LOC100505549 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC100505549 transcript NM_001242804.1:c. N/A Intron Variant
Gene: ATP8B1, ATPase phospholipid transporting 8B1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
ATP8B1 transcript NM_005603.5:c.2674G>A G [GGA] > R [AGA] Coding Sequence Variant
phospholipid-transporting ATPase IC NP_005594.1:p.Gly892Arg G (Gly) > R (Arg) Missense Variant
ATP8B1 transcript variant X1 XM_006722481.4:c.2674G>A G [GGA] > R [AGA] Coding Sequence Variant
phospholipid-transporting ATPase IC isoform X1 XP_006722544.1:p.Gly892Arg G (Gly) > R (Arg) Missense Variant
ATP8B1 transcript variant X2 XM_011526023.3:c.2560G>A G [GGA] > R [AGA] Coding Sequence Variant
phospholipid-transporting ATPase IC isoform X2 XP_011524325.1:p.Gly854Arg G (Gly) > R (Arg) Missense 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: T (allele ID: 22302 )
ClinVar Accession Disease Names Clinical Significance
RCV000007685.5 Progressive intrahepatic cholestasis Pathogenic
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 246104 C=0.99998 T=0.00002
gnomAD - Exomes European Sub 133868 C=0.99998 T=0.00002
gnomAD - Exomes Asian Sub 48028 C=1.0000 T=0.0000
gnomAD - Exomes American Sub 33580 C=1.0000 T=0.0000
gnomAD - Exomes African Sub 15300 C=1.0000 T=0.0000
gnomAD - Exomes Ashkenazi Jewish Sub 9844 C=1.000 T=0.000
gnomAD - Exomes Other Sub 5484 C=1.000 T=0.000
TopMed Global Study-wide 125568 C=0.99998 T=0.00002
ExAC Global Study-wide 121154 C=0.99998 T=0.00002
ExAC Europe Sub 73220 C=1.0000 T=0.0000
ExAC Asian Sub 25112 C=1.0000 T=0.0000
ExAC American Sub 11530 C=1.0000 T=0.0000
ExAC African Sub 10386 C=1.0000 T=0.0000
ExAC Other Sub 906 C=1.00 T=0.00
gnomAD - Genomes Global Study-wide 30960 C=1.0000 T=0.0000
gnomAD - Genomes European Sub 18494 C=0.9999 T=0.0001
gnomAD - Genomes African Sub 8724 C=1.000 T=0.000
gnomAD - Genomes East Asian Sub 1620 C=1.000 T=0.000
gnomAD - Genomes Other Sub 982 C=1.00 T=0.00
gnomAD - Genomes American Sub 838 C=1.00 T=0.00
gnomAD - Genomes Ashkenazi Jewish Sub 302 C=1.00 T=0.00
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= T Note
GRCh38.p12 chr 18 NC_000018.10:g.57661207C= NC_000018.10:g.57661207C>T
GRCh37.p13 chr 18 NC_000018.9:g.55328439C= NC_000018.9:g.55328439C>T
ATP8B1 RefSeqGene NG_007148.2:g.146889G= NG_007148.2:g.146889G>A
ATP8B1 transcript NM_005603.5:c.2674G= NM_005603.5:c.2674G>A
ATP8B1 transcript variant X1 XM_006722481.4:c.2674G= XM_006722481.4:c.2674G>A
ATP8B1 transcript variant X2 XM_011526023.3:c.2560G= XM_011526023.3:c.2560G>A
phospholipid-transporting ATPase IC NP_005594.1:p.Gly892= NP_005594.1:p.Gly892Arg
phospholipid-transporting ATPase IC isoform X1 XP_006722544.1:p.Gly892= XP_006722544.1:p.Gly892Arg
phospholipid-transporting ATPase IC isoform X2 XP_011524325.1:p.Gly854= XP_011524325.1:p.Gly854Arg
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#.

7 SubSNP, 4 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 OMIM-CURATED-RECORDS ss263193513 Oct 28, 2010 (133)
2 EVA_EXAC ss1693161939 Apr 01, 2015 (144)
3 HUMAN_LONGEVITY ss2222164491 Dec 20, 2016 (150)
4 GNOMAD ss2743315450 Nov 08, 2017 (151)
5 GNOMAD ss2749964282 Nov 08, 2017 (151)
6 GNOMAD ss2957488495 Nov 08, 2017 (151)
7 TOPMED ss3281144689 Nov 08, 2017 (151)
8 ExAC NC_000018.9 - 55328439 Oct 12, 2018 (152)
9 gnomAD - Genomes NC_000018.9 - 55328439 Oct 12, 2018 (152)
10 gnomAD - Exomes NC_000018.9 - 55328439 Oct 12, 2018 (152)
11 TopMed NC_000018.10 - 57661207 Oct 12, 2018 (152)
12 ClinVar RCV000007685.5 Oct 12, 2018 (152)
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
3634660, 91190024, 9944441, ss1693161939, ss2743315450, ss2749964282, ss2957488495 NC_000018.9:55328438:C= NC_000018.10:57661206:C= (self)
171430491, ss263193513, ss2222164491, ss3281144689 NC_000018.10:57661206:C= NC_000018.10:57661206:C= (self)
3634660, 91190024, 9944441, ss1693161939, ss2743315450, ss2749964282, ss2957488495 NC_000018.9:55328438:C>T NC_000018.10:57661206:C>T (self)
RCV000007685.5, 171430491, ss263193513, ss2222164491, ss3281144689 NC_000018.10:57661206:C>T NC_000018.10:57661206: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 rs121909098
PMID Title Author Year Journal
9500542 A gene encoding a P-type ATPase mutated in two forms of hereditary cholestasis. Bull LN et al. 1998 Nature genetics

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.post63+3f7b20b