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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.

rs1456289275

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr19:38217502 (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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000004 (1/264690, TOPMED)
T=0.000013 (2/155908, GnomAD_exome)
T=0.00000 (0/10680, ALFA) (+ 1 more)
T=0.0002 (1/6404, 1000G_30x)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
DPF1 : 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 T=0.00000 1.0 0.0 0.0 N/A
European Sub 6962 C=1.0000 T=0.0000 1.0 0.0 0.0 N/A
African Sub 2294 C=1.0000 T=0.0000 1.0 0.0 0.0 N/A
African Others Sub 84 C=1.00 T=0.00 1.0 0.0 0.0 N/A
African American Sub 2210 C=1.0000 T=0.0000 1.0 0.0 0.0 N/A
Asian Sub 108 C=1.000 T=0.000 1.0 0.0 0.0 N/A
East Asian Sub 84 C=1.00 T=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 24 C=1.00 T=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 C=1.000 T=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 C=1.000 T=0.000 1.0 0.0 0.0 N/A
South Asian Sub 94 C=1.00 T=0.00 1.0 0.0 0.0 N/A
Other Sub 466 C=1.000 T=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 T=0.000004
gnomAD - Exomes Global Study-wide 155908 C=0.999987 T=0.000013
gnomAD - Exomes European Sub 76748 C=0.99999 T=0.00001
gnomAD - Exomes Asian Sub 33700 C=1.00000 T=0.00000
gnomAD - Exomes American Sub 24672 C=0.99996 T=0.00004
gnomAD - Exomes Ashkenazi Jewish Sub 8478 C=1.0000 T=0.0000
gnomAD - Exomes African Sub 7936 C=1.0000 T=0.0000
gnomAD - Exomes Other Sub 4374 C=1.0000 T=0.0000
Allele Frequency Aggregator Total Global 10680 C=1.00000 T=0.00000
Allele Frequency Aggregator European Sub 6962 C=1.0000 T=0.0000
Allele Frequency Aggregator African Sub 2294 C=1.0000 T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 C=1.000 T=0.000
Allele Frequency Aggregator Other Sub 466 C=1.000 T=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 C=1.000 T=0.000
Allele Frequency Aggregator Asian Sub 108 C=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 94 C=1.00 T=0.00
1000Genomes_30x Global Study-wide 6404 C=0.9998 T=0.0002
1000Genomes_30x African Sub 1786 C=1.0000 T=0.0000
1000Genomes_30x Europe Sub 1266 C=1.0000 T=0.0000
1000Genomes_30x South Asian Sub 1202 C=1.0000 T=0.0000
1000Genomes_30x East Asian Sub 1170 C=0.9991 T=0.0009
1000Genomes_30x American Sub 980 C=1.000 T=0.000
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 19 NC_000019.10:g.38217502C>T
GRCh37.p13 chr 19 NC_000019.9:g.38708142C>T
Gene: DPF1, double PHD fingers 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
DPF1 transcript variant 2 NM_004647.4:c.595+296G>A N/A Intron Variant
DPF1 transcript variant 5 NM_001363579.1:c.688G>A E [GAA] > K [AAA] Coding Sequence Variant
zinc finger protein neuro-d4 isoform e NP_001350508.1:p.Glu230Lys E (Glu) > K (Lys) Missense Variant
DPF1 transcript variant 1 NM_001135155.3:c.685G>A E [GAA] > K [AAA] Coding Sequence Variant
zinc finger protein neuro-d4 isoform a NP_001128627.2:p.Glu229Lys E (Glu) > K (Lys) Missense Variant
DPF1 transcript variant 4 NM_001289978.2:c.685G>A E [GAA] > K [AAA] Coding Sequence Variant
zinc finger protein neuro-d4 isoform d NP_001276907.2:p.Glu229Lys E (Glu) > K (Lys) Missense Variant
DPF1 transcript variant 3 NM_001135156.3:c.520G>A E [GAA] > K [AAA] Coding Sequence Variant
zinc finger protein neuro-d4 isoform c NP_001128628.1:p.Glu174Lys E (Glu) > K (Lys) Missense Variant
DPF1 transcript variant X15 XM_047439494.1:c.*71= N/A 3 Prime UTR Variant
DPF1 transcript variant X14 XM_006723410.2:c.220G>A E [GAA] > K [AAA] Coding Sequence Variant
zinc finger protein neuro-d4 isoform X13 XP_006723473.1:p.Glu74Lys E (Glu) > K (Lys) Missense Variant
DPF1 transcript variant X1 XM_006723407.3:c.688G>A E [GAA] > K [AAA] Coding Sequence Variant
zinc finger protein neuro-d4 isoform X1 XP_006723470.1:p.Glu230Lys E (Glu) > K (Lys) Missense Variant
DPF1 transcript variant X2 XM_006723408.4:c.682G>A E [GAA] > K [AAA] Coding Sequence Variant
zinc finger protein neuro-d4 isoform X2 XP_006723471.1:p.Glu228Lys E (Glu) > K (Lys) Missense Variant
DPF1 transcript variant X3 XM_047439490.1:c.679G>A E [GAA] > K [AAA] Coding Sequence Variant
zinc finger protein neuro-d4 isoform X3 XP_047295446.1:p.Glu227Lys E (Glu) > K (Lys) Missense Variant
DPF1 transcript variant X4 XM_024451731.2:c.682G>A E [GAA] > K [AAA] Coding Sequence Variant
zinc finger protein neuro-d4 isoform X4 XP_024307499.1:p.Glu228Lys E (Glu) > K (Lys) Missense Variant
DPF1 transcript variant X5 XM_047439491.1:c.679G>A E [GAA] > K [AAA] Coding Sequence Variant
zinc finger protein neuro-d4 isoform X5 XP_047295447.1:p.Glu227Lys E (Glu) > K (Lys) Missense Variant
DPF1 transcript variant X6 XM_047439492.1:c.688G>A E [GAA] > K [AAA] Coding Sequence Variant
zinc finger protein neuro-d4 isoform X6 XP_047295448.1:p.Glu230Lys E (Glu) > K (Lys) Missense Variant
DPF1 transcript variant X7 XM_011527356.2:c.685G>A E [GAA] > K [AAA] Coding Sequence Variant
zinc finger protein neuro-d4 isoform X7 XP_011525658.2:p.Glu229Lys E (Glu) > K (Lys) Missense Variant
DPF1 transcript variant X8 XM_011527357.3:c.682G>A E [GAA] > K [AAA] Coding Sequence Variant
zinc finger protein neuro-d4 isoform X8 XP_011525659.1:p.Glu228Lys E (Glu) > K (Lys) Missense Variant
DPF1 transcript variant X9 XM_047439493.1:c.688G>A E [GAA] > K [AAA] Coding Sequence Variant
zinc finger protein neuro-d4 isoform X9 XP_047295449.1:p.Glu230Lys E (Glu) > K (Lys) Missense Variant
DPF1 transcript variant X10 XM_005259289.3:c.685G>A E [GAA] > K [AAA] Coding Sequence Variant
zinc finger protein neuro-d4 isoform X10 XP_005259346.2:p.Glu229Lys E (Glu) > K (Lys) Missense Variant
DPF1 transcript variant X11 XM_005259292.6:c.682G>A E [GAA] > K [AAA] Coding Sequence Variant
zinc finger protein neuro-d4 isoform X11 XP_005259349.1:p.Glu228Lys E (Glu) > K (Lys) Missense Variant
DPF1 transcript variant X12 XM_011527358.3:c.520G>A E [GAA] > K [AAA] Coding Sequence Variant
zinc finger protein neuro-d4 isoform X12 XP_011525660.1:p.Glu174Lys E (Glu) > K (Lys) Missense Variant
DPF1 transcript variant X13 XM_006723409.3:c.220G>A E [GAA] > K [AAA] Coding Sequence Variant
zinc finger protein neuro-d4 isoform X13 XP_006723472.1:p.Glu74Lys E (Glu) > K (Lys) 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
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
GRCh38.p14 chr 19 NC_000019.10:g.38217502= NC_000019.10:g.38217502C>T
GRCh37.p13 chr 19 NC_000019.9:g.38708142= NC_000019.9:g.38708142C>T
DPF1 transcript variant X11 XM_005259292.6:c.682= XM_005259292.6:c.682G>A
DPF1 transcript variant X8 XM_005259292.5:c.682= XM_005259292.5:c.682G>A
DPF1 transcript variant X7 XM_005259292.4:c.682= XM_005259292.4:c.682G>A
DPF1 transcript variant X7 XM_005259292.3:c.682= XM_005259292.3:c.682G>A
DPF1 transcript variant X5 XM_005259292.2:c.682= XM_005259292.2:c.682G>A
DPF1 transcript variant X5 XM_005259292.1:c.682= XM_005259292.1:c.682G>A
DPF1 transcript variant X2 XM_006723408.4:c.682= XM_006723408.4:c.682G>A
DPF1 transcript variant X4 XM_006723408.3:c.682= XM_006723408.3:c.682G>A
DPF1 transcript variant X4 XM_006723408.2:c.682= XM_006723408.2:c.682G>A
DPF1 transcript variant X10 XM_006723408.1:c.682= XM_006723408.1:c.682G>A
DPF1 transcript variant X12 XM_011527358.3:c.520= XM_011527358.3:c.520G>A
DPF1 transcript variant X9 XM_011527358.2:c.520= XM_011527358.2:c.520G>A
DPF1 transcript variant X8 XM_011527358.1:c.520= XM_011527358.1:c.520G>A
DPF1 transcript variant X1 XM_006723407.3:c.688= XM_006723407.3:c.688G>A
DPF1 transcript variant X2 XM_006723407.2:c.688= XM_006723407.2:c.688G>A
DPF1 transcript variant X9 XM_006723407.1:c.688= XM_006723407.1:c.688G>A
DPF1 transcript variant 3 NM_001135156.3:c.520= NM_001135156.3:c.520G>A
DPF1 transcript variant 3 NM_001135156.2:c.520= NM_001135156.2:c.520G>A
DPF1 transcript variant 3 NM_001135156.1:c.520= NM_001135156.1:c.520G>A
DPF1 transcript variant X8 XM_011527357.3:c.682= XM_011527357.3:c.682G>A
DPF1 transcript variant X7 XM_011527357.2:c.682= XM_011527357.2:c.682G>A
DPF1 transcript variant X6 XM_011527357.1:c.682= XM_011527357.1:c.682G>A
DPF1 transcript variant 1 NM_001135155.3:c.685= NM_001135155.3:c.685G>A
DPF1 transcript variant 1 NM_001135155.2:c.766= NM_001135155.2:c.766G>A
DPF1 transcript variant 1 NM_001135155.1:c.766= NM_001135155.1:c.766G>A
DPF1 transcript variant X10 XM_005259289.3:c.685= XM_005259289.3:c.685G>A
DPF1 transcript variant X3 XM_005259289.2:c.766= XM_005259289.2:c.766G>A
DPF1 transcript variant X2 XM_005259289.1:c.766= XM_005259289.1:c.766G>A
DPF1 transcript variant X13 XM_006723409.3:c.220= XM_006723409.3:c.220G>A
DPF1 transcript variant X10 XM_006723409.2:c.220= XM_006723409.2:c.220G>A
DPF1 transcript variant X11 XM_006723409.1:c.220= XM_006723409.1:c.220G>A
DPF1 transcript variant 4 NM_001289978.2:c.685= NM_001289978.2:c.685G>A
DPF1 transcript variant 4 NM_001289978.1:c.766= NM_001289978.1:c.766G>A
DPF1 transcript variant X4 XM_024451731.2:c.682= XM_024451731.2:c.682G>A
DPF1 transcript variant X6 XM_024451731.1:c.682= XM_024451731.1:c.682G>A
DPF1 transcript variant X7 XM_011527356.2:c.685= XM_011527356.2:c.685G>A
DPF1 transcript variant X1 XM_011527356.1:c.766= XM_011527356.1:c.766G>A
DPF1 transcript variant X14 XM_006723410.2:c.220= XM_006723410.2:c.220G>A
DPF1 transcript variant X12 XM_006723410.1:c.220= XM_006723410.1:c.220G>A
DPF1 transcript variant 5 NM_001363579.1:c.688= NM_001363579.1:c.688G>A
DPF1 transcript variant X3 XM_047439490.1:c.679= XM_047439490.1:c.679G>A
DPF1 transcript variant X6 XM_047439492.1:c.688= XM_047439492.1:c.688G>A
DPF1 transcript variant X5 XM_047439491.1:c.679= XM_047439491.1:c.679G>A
DPF1 transcript variant X9 XM_047439493.1:c.688= XM_047439493.1:c.688G>A
DPF1 transcript variant X15 XM_047439494.1:c.*71= XM_047439494.1:c.*71G>A
zinc finger protein neuro-d4 isoform X11 XP_005259349.1:p.Glu228= XP_005259349.1:p.Glu228Lys
zinc finger protein neuro-d4 isoform X2 XP_006723471.1:p.Glu228= XP_006723471.1:p.Glu228Lys
zinc finger protein neuro-d4 isoform X12 XP_011525660.1:p.Glu174= XP_011525660.1:p.Glu174Lys
zinc finger protein neuro-d4 isoform X1 XP_006723470.1:p.Glu230= XP_006723470.1:p.Glu230Lys
zinc finger protein neuro-d4 isoform c NP_001128628.1:p.Glu174= NP_001128628.1:p.Glu174Lys
zinc finger protein neuro-d4 isoform X8 XP_011525659.1:p.Glu228= XP_011525659.1:p.Glu228Lys
zinc finger protein neuro-d4 isoform a NP_001128627.2:p.Glu229= NP_001128627.2:p.Glu229Lys
zinc finger protein neuro-d4 isoform X10 XP_005259346.2:p.Glu229= XP_005259346.2:p.Glu229Lys
zinc finger protein neuro-d4 isoform X13 XP_006723472.1:p.Glu74= XP_006723472.1:p.Glu74Lys
zinc finger protein neuro-d4 isoform d NP_001276907.2:p.Glu229= NP_001276907.2:p.Glu229Lys
zinc finger protein neuro-d4 isoform X4 XP_024307499.1:p.Glu228= XP_024307499.1:p.Glu228Lys
zinc finger protein neuro-d4 isoform X7 XP_011525658.2:p.Glu229= XP_011525658.2:p.Glu229Lys
zinc finger protein neuro-d4 isoform X13 XP_006723473.1:p.Glu74= XP_006723473.1:p.Glu74Lys
zinc finger protein neuro-d4 isoform e NP_001350508.1:p.Glu230= NP_001350508.1:p.Glu230Lys
zinc finger protein neuro-d4 isoform X3 XP_047295446.1:p.Glu227= XP_047295446.1:p.Glu227Lys
zinc finger protein neuro-d4 isoform X6 XP_047295448.1:p.Glu230= XP_047295448.1:p.Glu230Lys
zinc finger protein neuro-d4 isoform X5 XP_047295447.1:p.Glu227= XP_047295447.1:p.Glu227Lys
zinc finger protein neuro-d4 isoform X9 XP_047295449.1:p.Glu230= XP_047295449.1:p.Glu230Lys
DPF1 transcript variant 2 NM_004647.2:c.676+296= NM_004647.2:c.676+296G>A
DPF1 transcript variant 2 NM_004647.4:c.595+296= NM_004647.4:c.595+296G>A
zinc finger protein neuro-d4 isoform a NP_001128627.1:p.Glu256= NP_001128627.1:p.Glu256Lys
zinc finger protein neuro-d4 isoform X3 XP_005259346.1:p.Glu256= XP_005259346.1:p.Glu256Lys
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#.

3 SubSNP, 4 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss2743946813 Nov 08, 2017 (151)
2 TOPMED ss5074448373 Apr 26, 2021 (155)
3 1000G_HIGH_COVERAGE ss5612917997 Oct 16, 2022 (156)
4 1000Genomes_30x NC_000019.10 - 38217502 Oct 16, 2022 (156)
5 gnomAD - Exomes NC_000019.9 - 38708142 Jul 13, 2019 (153)
6 TopMed NC_000019.10 - 38217502 Apr 26, 2021 (155)
7 ALFA NC_000019.10 - 38217502 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
13260978, ss2743946813 NC_000019.9:38708141:C:T NC_000019.10:38217501:C:T (self)
100443932, 289994037, 3629071178, ss5074448373, ss5612917997 NC_000019.10:38217501:C:T NC_000019.10:38217501: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.

No publications for rs1456289275

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