Skip to main page content

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.


Current Build 151

Released July 17, 2018

Homo sapiens
chr18:22181504 (GRCh38.p7) 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.

Variation Type
SNV Single Nucleotide Variation
Clinical Significance
Reported in ClinVar
Gene : Consequence
GATA6 : Missense Variant
1 citation
Genomic View
See rs on genome

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.p7 chr 18 NC_000018.10:g.22181504A>G
GRCh37.p13 chr 18 NC_000018.9:g.19761465A>G
GATA6 RefSeqGene NG_032677.1:g.17062A>G
Gene: GATA6, GATA binding protein 6 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
GATA6 transcript NM_005257.5:c.135...


T [ACC] > A [GCC] Coding Sequence Variant
transcription factor GATA-6 NP_005248.2:p.Thr...


T (Thr) > A (Ala) Missense 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: G (allele ID: 39167 )
ClinVar Accession Disease Names Clinical Significance
RCV000023133.3 Pancreatic agenesis and congenital heart disease Pathogenic

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").


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 A= G Note
GRCh38.p7 chr 18 NC_000018.10:g.22181504A= NC_000018.10:g.22181504A>G
GRCh37.p13 chr 18 NC_000018.9:g.19761465A= NC_000018.9:g.19761465A>G
GATA6 RefSeqGene NG_032677.1:g.17062A= NG_032677.1:g.17062A>G
GATA6 transcript NM_005257.5:c.1354A= NM_005257.5:c.1354A>G
GATA6 transcript NM_005257.4:c.1354A= NM_005257.4:c.1354A>G
transcription factor GATA-6 NP_005248.2:p.Thr452= NP_005248.2:p.Thr452Ala

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#.

3 SubSNP, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 OMIM-CURATED-RECORDS ss825077399 Jun 20, 2013 (137)
2 ILLUMINA ss1959791648 Feb 12, 2016 (147)
3 ILLUMINA ss3021828452 Nov 08, 2017 (151)
4 ClinVar RCV000023133.3 Jul 20, 2018 (151)

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
ss1959791648, ss3021828452 NC_000018.9:19761464:A= NC_000018.10:22181503:A= (self)
ss825077399 NC_000018.10:22181503:A= NC_000018.10:22181503:A= (self)
ss1959791648, ss3021828452 NC_000018.9:19761464:A>G NC_000018.10:22181503:A>G (self)
RCV000023133.3, ss825077399 NC_000018.10:22181503:A>G NC_000018.10:22181503:A>G (self)

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

1 citation for rs387906817
PMID Title Author Year Journal
22158542 GATA6 haploinsufficiency causes pancreatic agenesis in humans. Allen HL et al. 2011 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: 0.1.4.post833+d3ba21e