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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 Aliases 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.


Current Build 153

Released July 9, 2019

Homo sapiens
chr2:25164783 (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.

Variation Type
SNV Single Nucleotide Variation
T=0.00003 (7/250430, GnomAD_exome)
T=0.00002 (3/125568, TOPMED)
T=0.00003 (3/119554, ExAC) (+ 1 more)
T=0.0000 (1/31414, GnomAD)
Clinical Significance
Reported in ClinVar
Gene : Consequence
POMC : 5 Prime UTR Variant
2 citations
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.p12 chr 2 NC_000002.12:g.25164783G>T
GRCh37.p13 chr 2 NC_000002.11:g.25387652G>T
POMC RefSeqGene NG_008997.1:g.8908C>A
Gene: POMC, proopiomelanocortin (minus strand)
Molecule type Change Amino acid[Codon] SO Term
POMC transcript variant 1 NM_001035256.2:c.-11= N/A 5 Prime UTR Variant
POMC transcript variant 2 NM_000939.4:c.-11= N/A 5 Prime UTR Variant
POMC transcript variant 4 NM_001319205.2:c.-11= N/A 5 Prime UTR Variant
POMC transcript variant 3 NM_001319204.2:c.-11= N/A 5 Prime UTR 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: T (allele ID: 28394 )
ClinVar Accession Disease Names Clinical Significance
RCV000014283.21 Proopiomelanocortin deficiency 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").

Study Population Group Sample Size Ref Allele Alt Allele
gnomAD - Exomes Global Study-wide 250430 G=0.99997 T=0.00003
gnomAD - Exomes European Sub 134674 G=0.99995 T=0.00005
gnomAD - Exomes Asian Sub 48992 G=1.0000 T=0.0000
gnomAD - Exomes American Sub 34578 G=1.0000 T=0.0000
gnomAD - Exomes African Sub 16012 G=1.0000 T=0.0000
gnomAD - Exomes Ashkenazi Jewish Sub 10054 G=1.0000 T=0.0000
gnomAD - Exomes Other Sub 6120 G=1.000 T=0.000
TopMed Global Study-wide 125568 G=0.99998 T=0.00002
ExAC Global Study-wide 119554 G=0.99997 T=0.00003
ExAC Europe Sub 72062 G=1.0000 T=0.0000
ExAC Asian Sub 25118 G=1.0000 T=0.0000
ExAC American Sub 11538 G=1.0000 T=0.0000
ExAC African Sub 9942 G=1.000 T=0.000
ExAC Other Sub 894 G=1.00 T=0.00
gnomAD - Genomes Global Study-wide 31414 G=1.0000 T=0.0000
gnomAD - Genomes European Sub 18910 G=0.9999 T=0.0001
gnomAD - Genomes African Sub 8718 G=1.000 T=0.000
gnomAD - Genomes East Asian Sub 1560 G=1.000 T=0.000
gnomAD - Genomes Other Sub 1088 G=1.000 T=0.000
gnomAD - Genomes American Sub 848 G=1.00 T=0.00
gnomAD - Genomes Ashkenazi Jewish Sub 290 G=1.00 T=0.00

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 G= T Note
GRCh38.p12 chr 2 NC_000002.12:g.25164783= NC_000002.12:g.25164783G>T
GRCh37.p13 chr 2 NC_000002.11:g.25387652= NC_000002.11:g.25387652G>T
POMC RefSeqGene NG_008997.1:g.8908= NG_008997.1:g.8908C>A
POMC transcript variant 2 NM_000939.4:c.-11= NM_000939.4:c.-11C>A
POMC transcript variant 2 NM_000939.3:c.-11= NM_000939.3:c.-11C>A
POMC transcript variant 2 NM_000939.2:c.-11= NM_000939.2:c.-11C>A
POMC transcript variant 1 NM_001035256.2:c.-11= NM_001035256.2:c.-11C>A
POMC transcript variant 1 NM_001035256.1:c.-11= NM_001035256.1:c.-11C>A
POMC transcript variant 3 NM_001319204.2:c.-11= NM_001319204.2:c.-11C>A
POMC transcript variant 3 NM_001319204.1:c.-11= NM_001319204.1:c.-11C>A
POMC transcript variant 4 NM_001319205.2:c.-11= NM_001319205.2:c.-11C>A
POMC transcript variant 4 NM_001319205.1:c.-11= NM_001319205.1:c.-11C>A

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#.

9 SubSNP, 4 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 EVA_EXAC ss1686211662 Apr 01, 2015 (144)
2 TOPMED ss2394312712 Dec 20, 2016 (150)
3 GNOMAD ss2732517336 Nov 08, 2017 (151)
4 GNOMAD ss2746636561 Nov 08, 2017 (151)
5 GNOMAD ss2770920398 Nov 08, 2017 (151)
6 ILLUMINA ss3021950441 Nov 08, 2017 (151)
7 TOPMED ss3302030211 Nov 08, 2017 (151)
8 ILLUMINA ss3652379483 Oct 11, 2018 (152)
9 ILLUMINA ss3725766104 Jul 12, 2019 (153)
10 ExAC NC_000002.11 - 25387652 Oct 11, 2018 (152)
11 gnomAD - Genomes NC_000002.11 - 25387652 Jul 12, 2019 (153)
12 gnomAD - Exomes NC_000002.11 - 25387652 Jul 12, 2019 (153)
13 TopMed NC_000002.12 - 25164783 Oct 11, 2018 (152)
14 ClinVar RCV000014283.21 Oct 11, 2018 (152)

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
6074443, 19738472, 1559024, ss1686211662, ss2394312712, ss2732517336, ss2746636561, ss2770920398, ss3021950441, ss3652379483 NC_000002.11:25387651:G:T NC_000002.12:25164782:G:T (self)
RCV000014283.21, 188194119, ss3302030211, ss3725766104 NC_000002.12:25164782:G:T NC_000002.12:25164782:G:T (self)

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

2 citations for rs753856820
PMID Title Author Year Journal
9620771 Severe early-onset obesity, adrenal insufficiency and red hair pigmentation caused by POMC mutations in humans. Krude H et al. 1998 Nature genetics
14557433 Obesity due to proopiomelanocortin deficiency: three new cases and treatment trials with thyroid hormone and ACTH4-10. Krude H et al. 2003 The Journal of clinical endocrinology and metabolism

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.post308+0fe9b3b