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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs1476643245

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr20:41357412 (GRCh38.p14) 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>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000004 (1/264690, TOPMED)
A=0.000004 (1/251154, GnomAD_exome)
A=0.00000 (0/10680, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LPIN3 : Missense Variant
Publications
0 citations
Genomic View
See rs on genome

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: 20231103111315
Population Group Sample Size Ref Allele Alt Allele Ref HMOZ Alt HMOZ HTRZ HWEP
Total Global 10680 C=1.00000 A=0.00000 1.0 0.0 0.0 N/A
European Sub 6962 C=1.0000 A=0.0000 1.0 0.0 0.0 N/A
African Sub 2294 C=1.0000 A=0.0000 1.0 0.0 0.0 N/A
African Others Sub 84 C=1.00 A=0.00 1.0 0.0 0.0 N/A
African American Sub 2210 C=1.0000 A=0.0000 1.0 0.0 0.0 N/A
Asian Sub 108 C=1.000 A=0.000 1.0 0.0 0.0 N/A
East Asian Sub 84 C=1.00 A=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 24 C=1.00 A=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 C=1.000 A=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 C=1.000 A=0.000 1.0 0.0 0.0 N/A
South Asian Sub 94 C=1.00 A=0.00 1.0 0.0 0.0 N/A
Other Sub 466 C=1.000 A=0.000 1.0 0.0 0.0 N/A


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 C=0.999996 A=0.000004
gnomAD - Exomes Global Study-wide 251154 C=0.999996 A=0.000004
gnomAD - Exomes European Sub 135120 C=1.000000 A=0.000000
gnomAD - Exomes Asian Sub 49010 C=1.00000 A=0.00000
gnomAD - Exomes American Sub 34570 C=0.99997 A=0.00003
gnomAD - Exomes African Sub 16256 C=1.00000 A=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10068 C=1.00000 A=0.00000
gnomAD - Exomes Other Sub 6130 C=1.0000 A=0.0000
Allele Frequency Aggregator Total Global 10680 C=1.00000 A=0.00000
Allele Frequency Aggregator European Sub 6962 C=1.0000 A=0.0000
Allele Frequency Aggregator African Sub 2294 C=1.0000 A=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 C=1.000 A=0.000
Allele Frequency Aggregator Other Sub 466 C=1.000 A=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 C=1.000 A=0.000
Allele Frequency Aggregator Asian Sub 108 C=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 94 C=1.00 A=0.00
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.p14 chr 20 NC_000020.11:g.41357412C>A
GRCh37.p13 chr 20 NC_000020.10:g.39986052C>A
Gene: LPIN3, lipin 3 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LPIN3 transcript variant 1 NM_001301860.2:c.2007C>A H [CAC] > Q [CAA] Coding Sequence Variant
phosphatidate phosphatase LPIN3 isoform 1 NP_001288789.1:p.His669Gln H (His) > Q (Gln) Missense Variant
LPIN3 transcript variant 3 NM_022896.3:c.2004C>A H [CAC] > Q [CAA] Coding Sequence Variant
phosphatidate phosphatase LPIN3 isoform 2 NP_075047.1:p.His668Gln H (His) > Q (Gln) Missense Variant
LPIN3 transcript variant 2 NR_126051.2:n.2192C>A N/A Non Coding Transcript Variant
LPIN3 transcript variant X23 XM_005260516.3:c. N/A Genic Downstream Transcript Variant
LPIN3 transcript variant X21 XM_006723863.3:c. N/A Genic Downstream Transcript Variant
LPIN3 transcript variant X22 XM_011529006.3:c. N/A Genic Downstream Transcript Variant
LPIN3 transcript variant X1 XM_011528999.4:c.2007C>A H [CAC] > Q [CAA] Coding Sequence Variant
phosphatidate phosphatase LPIN3 isoform X1 XP_011527301.1:p.His669Gln H (His) > Q (Gln) Missense Variant
LPIN3 transcript variant X2 XM_011528996.3:c.2007C>A H [CAC] > Q [CAA] Coding Sequence Variant
phosphatidate phosphatase LPIN3 isoform X1 XP_011527298.1:p.His669Gln H (His) > Q (Gln) Missense Variant
LPIN3 transcript variant X3 XM_011528998.4:c.2007C>A H [CAC] > Q [CAA] Coding Sequence Variant
phosphatidate phosphatase LPIN3 isoform X1 XP_011527300.1:p.His669Gln H (His) > Q (Gln) Missense Variant
LPIN3 transcript variant X4 XM_011528997.4:c.2007C>A H [CAC] > Q [CAA] Coding Sequence Variant
phosphatidate phosphatase LPIN3 isoform X1 XP_011527299.1:p.His669Gln H (His) > Q (Gln) Missense Variant
LPIN3 transcript variant X5 XM_011529000.3:c.2004C>A H [CAC] > Q [CAA] Coding Sequence Variant
phosphatidate phosphatase LPIN3 isoform X2 XP_011527302.1:p.His668Gln H (His) > Q (Gln) Missense Variant
LPIN3 transcript variant X6 XM_047440383.1:c.2004C>A H [CAC] > Q [CAA] Coding Sequence Variant
phosphatidate phosphatase LPIN3 isoform X2 XP_047296339.1:p.His668Gln H (His) > Q (Gln) Missense Variant
LPIN3 transcript variant X7 XM_047440384.1:c.2007C>A H [CAC] > Q [CAA] Coding Sequence Variant
phosphatidate phosphatase LPIN3 isoform X3 XP_047296340.1:p.His669Gln H (His) > Q (Gln) Missense Variant
LPIN3 transcript variant X8 XM_047440385.1:c.2007C>A H [CAC] > Q [CAA] Coding Sequence Variant
phosphatidate phosphatase LPIN3 isoform X3 XP_047296341.1:p.His669Gln H (His) > Q (Gln) Missense Variant
LPIN3 transcript variant X9 XM_047440386.1:c.2004C>A H [CAC] > Q [CAA] Coding Sequence Variant
phosphatidate phosphatase LPIN3 isoform X4 XP_047296342.1:p.His668Gln H (His) > Q (Gln) Missense Variant
LPIN3 transcript variant X10 XM_047440387.1:c.2004C>A H [CAC] > Q [CAA] Coding Sequence Variant
phosphatidate phosphatase LPIN3 isoform X4 XP_047296343.1:p.His668Gln H (His) > Q (Gln) Missense Variant
LPIN3 transcript variant X11 XM_011529001.3:c.2007C>A H [CAC] > Q [CAA] Coding Sequence Variant
phosphatidate phosphatase LPIN3 isoform X5 XP_011527303.1:p.His669Gln H (His) > Q (Gln) Missense Variant
LPIN3 transcript variant X12 XM_047440388.1:c.2004C>A H [CAC] > Q [CAA] Coding Sequence Variant
phosphatidate phosphatase LPIN3 isoform X6 XP_047296344.1:p.His668Gln H (His) > Q (Gln) Missense Variant
LPIN3 transcript variant X14 XM_011529002.4:c.1611C>A H [CAC] > Q [CAA] Coding Sequence Variant
phosphatidate phosphatase LPIN3 isoform X7 XP_011527304.1:p.His537Gln H (His) > Q (Gln) Missense Variant
LPIN3 transcript variant X15 XM_011529003.2:c.2007C>A H [CAC] > Q [CAA] Coding Sequence Variant
phosphatidate phosphatase LPIN3 isoform X8 XP_011527305.1:p.His669Gln H (His) > Q (Gln) Missense Variant
LPIN3 transcript variant X17 XM_011529004.2:c.2007C>A H [CAC] > Q [CAA] Coding Sequence Variant
phosphatidate phosphatase LPIN3 isoform X9 XP_011527306.1:p.His669Gln H (His) > Q (Gln) Missense Variant
LPIN3 transcript variant X18 XM_047440389.1:c.2007C>A H [CAC] > Q [CAA] Coding Sequence Variant
phosphatidate phosphatase LPIN3 isoform X10 XP_047296345.1:p.His669Gln H (His) > Q (Gln) Missense Variant
LPIN3 transcript variant X20 XM_011529005.3:c.2007C>A H [CAC] > Q [CAA] Coding Sequence Variant
phosphatidate phosphatase LPIN3 isoform X11 XP_011527307.1:p.His669Gln H (His) > Q (Gln) Missense Variant
LPIN3 transcript variant X13 XR_007067476.1:n.2197C>A N/A Non Coding Transcript Variant
LPIN3 transcript variant X16 XR_936610.3:n.2197C>A N/A Non Coding Transcript Variant
LPIN3 transcript variant X19 XR_430311.2:n.2197C>A N/A Non Coding Transcript 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
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= A
GRCh38.p14 chr 20 NC_000020.11:g.41357412= NC_000020.11:g.41357412C>A
GRCh37.p13 chr 20 NC_000020.10:g.39986052= NC_000020.10:g.39986052C>A
LPIN3 transcript variant X4 XM_011528997.4:c.2007= XM_011528997.4:c.2007C>A
LPIN3 transcript variant X2 XM_011528997.3:c.2007= XM_011528997.3:c.2007C>A
LPIN3 transcript variant X2 XM_011528997.2:c.2007= XM_011528997.2:c.2007C>A
LPIN3 transcript variant X2 XM_011528997.1:c.2007= XM_011528997.1:c.2007C>A
LPIN3 transcript variant X1 XM_011528999.4:c.2007= XM_011528999.4:c.2007C>A
LPIN3 transcript variant X4 XM_011528999.3:c.2007= XM_011528999.3:c.2007C>A
LPIN3 transcript variant X4 XM_011528999.2:c.2007= XM_011528999.2:c.2007C>A
LPIN3 transcript variant X4 XM_011528999.1:c.2007= XM_011528999.1:c.2007C>A
LPIN3 transcript variant X3 XM_011528998.4:c.2007= XM_011528998.4:c.2007C>A
LPIN3 transcript variant X3 XM_011528998.3:c.2007= XM_011528998.3:c.2007C>A
LPIN3 transcript variant X3 XM_011528998.2:c.2007= XM_011528998.2:c.2007C>A
LPIN3 transcript variant X3 XM_011528998.1:c.2007= XM_011528998.1:c.2007C>A
LPIN3 transcript variant X14 XM_011529002.4:c.1611= XM_011529002.4:c.1611C>A
LPIN3 transcript variant X8 XM_011529002.3:c.1611= XM_011529002.3:c.1611C>A
LPIN3 transcript variant X9 XM_011529002.2:c.1611= XM_011529002.2:c.1611C>A
LPIN3 transcript variant X8 XM_011529002.1:c.1611= XM_011529002.1:c.1611C>A
LPIN3 transcript variant X2 XM_011528996.3:c.2007= XM_011528996.3:c.2007C>A
LPIN3 transcript variant X1 XM_011528996.2:c.2007= XM_011528996.2:c.2007C>A
LPIN3 transcript variant X1 XM_011528996.1:c.2007= XM_011528996.1:c.2007C>A
LPIN3 transcript variant X5 XM_011529000.3:c.2004= XM_011529000.3:c.2004C>A
LPIN3 transcript variant X5 XM_011529000.2:c.2004= XM_011529000.2:c.2004C>A
LPIN3 transcript variant X5 XM_011529000.1:c.2004= XM_011529000.1:c.2004C>A
LPIN3 transcript variant 3 NM_022896.3:c.2004= NM_022896.3:c.2004C>A
LPIN3 transcript variant 3 NM_022896.2:c.2004= NM_022896.2:c.2004C>A
LPIN3 transcript variant 3 NM_022896.1:c.2004= NM_022896.1:c.2004C>A
LPIN3 transcript variant X11 XM_011529001.3:c.2007= XM_011529001.3:c.2007C>A
LPIN3 transcript variant X6 XM_011529001.2:c.2007= XM_011529001.2:c.2007C>A
LPIN3 transcript variant X7 XM_011529001.1:c.2007= XM_011529001.1:c.2007C>A
LPIN3 transcript variant X16 XR_936610.3:n.2197= XR_936610.3:n.2197C>A
LPIN3 transcript variant X10 XR_936610.2:n.2163= XR_936610.2:n.2163C>A
LPIN3 transcript variant X11 XR_936610.1:n.2163= XR_936610.1:n.2163C>A
LPIN3 transcript variant X20 XM_011529005.3:c.2007= XM_011529005.3:c.2007C>A
LPIN3 transcript variant X13 XM_011529005.2:c.2007= XM_011529005.2:c.2007C>A
LPIN3 transcript variant X13 XM_011529005.1:c.2007= XM_011529005.1:c.2007C>A
LPIN3 transcript variant 1 NM_001301860.2:c.2007= NM_001301860.2:c.2007C>A
LPIN3 transcript variant 1 NM_001301860.1:c.2007= NM_001301860.1:c.2007C>A
LPIN3 transcript variant 2 NR_126051.2:n.2192= NR_126051.2:n.2192C>A
LPIN3 transcript variant 2 NR_126051.1:n.2160= NR_126051.1:n.2160C>A
LPIN3 transcript variant X15 XM_011529003.2:c.2007= XM_011529003.2:c.2007C>A
LPIN3 transcript variant X9 XM_011529003.1:c.2007= XM_011529003.1:c.2007C>A
LPIN3 transcript variant X17 XM_011529004.2:c.2007= XM_011529004.2:c.2007C>A
LPIN3 transcript variant X11 XM_011529004.1:c.2007= XM_011529004.1:c.2007C>A
LPIN3 transcript variant X19 XR_430311.2:n.2197= XR_430311.2:n.2197C>A
LPIN3 transcript variant X12 XR_430311.1:n.2163= XR_430311.1:n.2163C>A
LPIN3 transcript variant X7 XM_047440384.1:c.2007= XM_047440384.1:c.2007C>A
LPIN3 transcript variant X9 XM_047440386.1:c.2004= XM_047440386.1:c.2004C>A
LPIN3 transcript variant X6 XM_047440383.1:c.2004= XM_047440383.1:c.2004C>A
LPIN3 transcript variant X8 XM_047440385.1:c.2007= XM_047440385.1:c.2007C>A
LPIN3 transcript variant X10 XM_047440387.1:c.2004= XM_047440387.1:c.2004C>A
LPIN3 transcript variant X12 XM_047440388.1:c.2004= XM_047440388.1:c.2004C>A
LPIN3 transcript variant X13 XR_007067476.1:n.2197= XR_007067476.1:n.2197C>A
LPIN3 transcript variant X18 XM_047440389.1:c.2007= XM_047440389.1:c.2007C>A
phosphatidate phosphatase LPIN3 isoform X1 XP_011527299.1:p.His669= XP_011527299.1:p.His669Gln
phosphatidate phosphatase LPIN3 isoform X1 XP_011527301.1:p.His669= XP_011527301.1:p.His669Gln
phosphatidate phosphatase LPIN3 isoform X1 XP_011527300.1:p.His669= XP_011527300.1:p.His669Gln
phosphatidate phosphatase LPIN3 isoform X7 XP_011527304.1:p.His537= XP_011527304.1:p.His537Gln
phosphatidate phosphatase LPIN3 isoform X1 XP_011527298.1:p.His669= XP_011527298.1:p.His669Gln
phosphatidate phosphatase LPIN3 isoform X2 XP_011527302.1:p.His668= XP_011527302.1:p.His668Gln
phosphatidate phosphatase LPIN3 isoform 2 NP_075047.1:p.His668= NP_075047.1:p.His668Gln
phosphatidate phosphatase LPIN3 isoform X5 XP_011527303.1:p.His669= XP_011527303.1:p.His669Gln
phosphatidate phosphatase LPIN3 isoform X11 XP_011527307.1:p.His669= XP_011527307.1:p.His669Gln
phosphatidate phosphatase LPIN3 isoform 1 NP_001288789.1:p.His669= NP_001288789.1:p.His669Gln
phosphatidate phosphatase LPIN3 isoform X8 XP_011527305.1:p.His669= XP_011527305.1:p.His669Gln
phosphatidate phosphatase LPIN3 isoform X9 XP_011527306.1:p.His669= XP_011527306.1:p.His669Gln
phosphatidate phosphatase LPIN3 isoform X3 XP_047296340.1:p.His669= XP_047296340.1:p.His669Gln
phosphatidate phosphatase LPIN3 isoform X4 XP_047296342.1:p.His668= XP_047296342.1:p.His668Gln
phosphatidate phosphatase LPIN3 isoform X2 XP_047296339.1:p.His668= XP_047296339.1:p.His668Gln
phosphatidate phosphatase LPIN3 isoform X3 XP_047296341.1:p.His669= XP_047296341.1:p.His669Gln
phosphatidate phosphatase LPIN3 isoform X4 XP_047296343.1:p.His668= XP_047296343.1:p.His668Gln
phosphatidate phosphatase LPIN3 isoform X6 XP_047296344.1:p.His668= XP_047296344.1:p.His668Gln
phosphatidate phosphatase LPIN3 isoform X10 XP_047296345.1:p.His669= XP_047296345.1:p.His669Gln
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#.

2 SubSNP, 3 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss2744607699 Nov 08, 2017 (151)
2 TOPMED ss5089034656 Apr 26, 2021 (155)
3 gnomAD - Exomes NC_000020.10 - 39986052 Jul 13, 2019 (153)
4 TopMed NC_000020.11 - 41357412 Apr 26, 2021 (155)
5 ALFA NC_000020.11 - 41357412 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
13929318, ss2744607699 NC_000020.10:39986051:C:A NC_000020.11:41357411:C:A (self)
364143601, 1954795286, ss5089034656 NC_000020.11:41357411:C:A NC_000020.11:41357411:C: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 rs1476643245

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.post820+afb47a3d