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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.

rs146053800

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr12:102197083 (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
G>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000045 (12/264690, TOPMED)
A=0.000032 (8/250578, GnomAD_exome)
A=0.000036 (5/139888, GnomAD) (+ 3 more)
A=0.000050 (6/120344, ExAC)
A=0.00000 (0/14050, ALFA)
A=0.00008 (1/13006, GO-ESP)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
PMCH : Missense Variant
PARPBP : Non Coding Transcript Variant
Publications
0 citations
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 12 NC_000012.12:g.102197083G>A
GRCh37.p13 chr 12 NC_000012.11:g.102590861G>A
Gene: PARPBP, PARP1 binding protein (plus strand)
Molecule type Change Amino acid[Codon] SO Term
PARPBP transcript variant 10 NM_001382723.1:c.*792= N/A 3 Prime UTR Variant
PARPBP transcript variant 17 NM_001382732.1:c.*1060= N/A 3 Prime UTR Variant
PARPBP transcript variant 13 NM_001382726.1:c.*792= N/A 3 Prime UTR Variant
PARPBP transcript variant 12 NM_001382725.1:c.*1124= N/A 3 Prime UTR Variant
PARPBP transcript variant 9 NM_001382722.1:c.*792= N/A 3 Prime UTR Variant
PARPBP transcript variant 2 NM_017915.5:c.*792= N/A 3 Prime UTR Variant
PARPBP transcript variant 14 NM_001382728.1:c.*792= N/A 3 Prime UTR Variant
PARPBP transcript variant 11 NM_001382724.1:c.*792= N/A 3 Prime UTR Variant
PARPBP transcript variant 4 NM_001319994.2:c.*792= N/A 3 Prime UTR Variant
PARPBP transcript variant 8 NM_001382721.1:c.*792= N/A 3 Prime UTR Variant
PARPBP transcript variant 16 NM_001382731.1:c.*1124= N/A 3 Prime UTR Variant
PARPBP transcript variant 3 NM_001319993.2:c.*792= N/A 3 Prime UTR Variant
PARPBP transcript variant 15 NM_001382729.1:c.*1124= N/A 3 Prime UTR Variant
PARPBP transcript variant 1 NM_001319988.2:c.*792= N/A 3 Prime UTR Variant
PARPBP transcript variant 7 NM_001382735.1:c.*1060= N/A 3 Prime UTR Variant
PARPBP transcript variant 5 NM_001319995.3:c. N/A Genic Downstream Transcript Variant
PARPBP transcript variant 6 NM_001319996.2:c. N/A Genic Downstream Transcript Variant
PARPBP transcript variant X12 XM_011538515.1:c.*792= N/A 3 Prime UTR Variant
PARPBP transcript variant X3 XM_017019535.1:c.*792= N/A 3 Prime UTR Variant
PARPBP transcript variant X7 XM_011538514.2:c.*792= N/A 3 Prime UTR Variant
PARPBP transcript variant X11 XM_024449028.1:c.*792= N/A 3 Prime UTR Variant
PARPBP transcript variant X10 XM_017019541.2:c. N/A Genic Downstream Transcript Variant
PARPBP transcript variant X13 XR_001748775.2:n.2430G>A N/A Non Coding Transcript Variant
PARPBP transcript variant X14 XR_001748776.2:n.2294G>A N/A Non Coding Transcript Variant
Gene: PMCH, pro-melanin concentrating hormone (minus strand)
Molecule type Change Amino acid[Codon] SO Term
PMCH transcript NM_002674.4:c.338C>T A [GCT] > V [GTT] Coding Sequence Variant
pro-MCH preproprotein NP_002665.2:p.Ala113Val A (Ala) > V (Val) Missense Variant
PMCH transcript variant X1 XM_017019483.2:c.338C>T A [GCT] > V [GTT] Coding Sequence Variant
pro-MCH isoform X1 XP_016874972.1:p.Ala113Val A (Ala) > V (Val) 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.

Not Reported in ClinVar

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 14050 G=1.00000 A=0.00000
European Sub 9690 G=1.0000 A=0.0000
African Sub 2898 G=1.0000 A=0.0000
African Others Sub 114 G=1.000 A=0.000
African American Sub 2784 G=1.0000 A=0.0000
Asian Sub 112 G=1.000 A=0.000
East Asian Sub 86 G=1.00 A=0.00
Other Asian Sub 26 G=1.00 A=0.00
Latin American 1 Sub 146 G=1.000 A=0.000
Latin American 2 Sub 610 G=1.000 A=0.000
South Asian Sub 98 G=1.00 A=0.00
Other Sub 496 G=1.000 A=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
TopMed Global Study-wide 264690 G=0.999955 A=0.000045
gnomAD - Exomes Global Study-wide 250578 G=0.999968 A=0.000032
gnomAD - Exomes European Sub 134794 G=0.999978 A=0.000022
gnomAD - Exomes Asian Sub 48956 G=1.00000 A=0.00000
gnomAD - Exomes American Sub 34466 G=0.99997 A=0.00003
gnomAD - Exomes African Sub 16200 G=0.99975 A=0.00025
gnomAD - Exomes Ashkenazi Jewish Sub 10066 G=1.00000 A=0.00000
gnomAD - Exomes Other Sub 6096 G=1.0000 A=0.0000
gnomAD - Genomes Global Study-wide 139888 G=0.999964 A=0.000036
gnomAD - Genomes European Sub 75714 G=1.00000 A=0.00000
gnomAD - Genomes African Sub 41984 G=0.99990 A=0.00010
gnomAD - Genomes American Sub 13592 G=1.00000 A=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3320 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3128 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2150 G=0.9995 A=0.0005
ExAC Global Study-wide 120344 G=0.999950 A=0.000050
ExAC Europe Sub 72842 G=0.99996 A=0.00004
ExAC Asian Sub 25034 G=1.00000 A=0.00000
ExAC American Sub 11334 G=1.00000 A=0.00000
ExAC African Sub 10234 G=0.99971 A=0.00029
ExAC Other Sub 900 G=1.000 A=0.000
GO Exome Sequencing Project Global Study-wide 13006 G=0.99992 A=0.00008
GO Exome Sequencing Project European American Sub 8600 G=1.0000 A=0.0000
GO Exome Sequencing Project African American Sub 4406 G=0.9998 A=0.0002
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 G= A
GRCh38.p13 chr 12 NC_000012.12:g.102197083= NC_000012.12:g.102197083G>A
GRCh37.p13 chr 12 NC_000012.11:g.102590861= NC_000012.11:g.102590861G>A
PARPBP transcript variant 2 NM_017915.5:c.*792= NM_017915.5:c.*792G>A
PARPBP transcript variant 2 NM_017915.4:c.*792= NM_017915.4:c.*792G>A
PARPBP transcript NM_017915.3:c.*792= NM_017915.3:c.*792G>A
PMCH transcript NM_002674.4:c.338= NM_002674.4:c.338C>T
PMCH transcript NM_002674.3:c.338= NM_002674.3:c.338C>T
PMCH transcript NM_002674.2:c.338= NM_002674.2:c.338C>T
PARPBP transcript variant 1 NM_001319988.2:c.*792= NM_001319988.2:c.*792G>A
PARPBP transcript variant 1 NM_001319988.1:c.*792= NM_001319988.1:c.*792G>A
PARPBP transcript variant 3 NM_001319993.2:c.*792= NM_001319993.2:c.*792G>A
PARPBP transcript variant 3 NM_001319993.1:c.*792= NM_001319993.1:c.*792G>A
PARPBP transcript variant 4 NM_001319994.2:c.*792= NM_001319994.2:c.*792G>A
PARPBP transcript variant 4 NM_001319994.1:c.*792= NM_001319994.1:c.*792G>A
PARPBP transcript variant X7 XM_011538514.2:c.*792= XM_011538514.2:c.*792G>A
PARPBP transcript variant X13 XR_001748775.2:n.2430= XR_001748775.2:n.2430G>A
PARPBP transcript variant X14 XR_001748776.2:n.2294= XR_001748776.2:n.2294G>A
PMCH transcript variant X1 XM_017019483.2:c.338= XM_017019483.2:c.338C>T
PARPBP transcript variant X11 XM_024449028.1:c.*792= XM_024449028.1:c.*792G>A
PARPBP transcript variant 12 NM_001382725.1:c.*1124= NM_001382725.1:c.*1124G>A
PARPBP transcript variant X3 XM_017019535.1:c.*792= XM_017019535.1:c.*792G>A
PARPBP transcript variant 8 NM_001382721.1:c.*792= NM_001382721.1:c.*792G>A
PARPBP transcript variant 9 NM_001382722.1:c.*792= NM_001382722.1:c.*792G>A
PARPBP transcript variant 10 NM_001382723.1:c.*792= NM_001382723.1:c.*792G>A
PARPBP transcript variant 11 NM_001382724.1:c.*792= NM_001382724.1:c.*792G>A
PARPBP transcript variant 14 NM_001382728.1:c.*792= NM_001382728.1:c.*792G>A
PARPBP transcript variant X12 XM_011538515.1:c.*792= XM_011538515.1:c.*792G>A
PARPBP transcript variant 15 NM_001382729.1:c.*1124= NM_001382729.1:c.*1124G>A
PARPBP transcript variant 16 NM_001382731.1:c.*1124= NM_001382731.1:c.*1124G>A
PARPBP transcript variant 17 NM_001382732.1:c.*1060= NM_001382732.1:c.*1060G>A
PARPBP transcript variant 13 NM_001382726.1:c.*792= NM_001382726.1:c.*792G>A
PARPBP transcript variant 7 NR_135123.1:n.1731= NR_135123.1:n.1731G>A
PARPBP transcript variant 7 NM_001382735.1:c.*1060= NM_001382735.1:c.*1060G>A
pro-MCH preproprotein NP_002665.2:p.Ala113= NP_002665.2:p.Ala113Val
pro-MCH isoform X1 XP_016874972.1:p.Ala113= XP_016874972.1:p.Ala113Val
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#.

9 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 NHLBI-ESP ss342365167 May 09, 2011 (134)
2 EVA_EXAC ss1691072046 Apr 01, 2015 (144)
3 HUMAN_LONGEVITY ss2192686964 Dec 20, 2016 (150)
4 TOPMED ss2356706066 Dec 20, 2016 (150)
5 GNOMAD ss2740076375 Nov 08, 2017 (151)
6 TOPMED ss3180107751 Nov 08, 2017 (151)
7 EVA ss3824762837 Apr 27, 2020 (154)
8 GNOMAD ss4257971869 Apr 26, 2021 (155)
9 TOPMED ss4930688563 Apr 26, 2021 (155)
10 ExAC NC_000012.11 - 102590861 Oct 12, 2018 (152)
11 gnomAD - Genomes NC_000012.12 - 102197083 Apr 26, 2021 (155)
12 gnomAD - Exomes NC_000012.11 - 102590861 Jul 13, 2019 (153)
13 GO Exome Sequencing Project NC_000012.11 - 102590861 Oct 12, 2018 (152)
14 TopMed NC_000012.12 - 102197083 Apr 26, 2021 (155)
15 ALFA NC_000012.12 - 102197083 Apr 26, 2021 (155)
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
1383081, 9312893, 1220287, ss342365167, ss1691072046, ss2356706066, ss2740076375, ss3824762837 NC_000012.11:102590860:G:A NC_000012.12:102197082:G:A (self)
417599702, 91499674, 146234220, 12806164312, ss2192686964, ss3180107751, ss4257971869, ss4930688563 NC_000012.12:102197082:G:A NC_000012.12:102197082:G:A (self)
Help

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

No publications for rs146053800

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