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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.

rs781574321

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr19:1466230 (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
G>A / G>C
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000121 (32/264690, TOPMED)
A=0.000020 (3/146810, GnomAD_exome)
A=0.00003 (1/34110, ExAC) (+ 5 more)
A=0.00004 (1/28254, 14KJPN)
A=0.00006 (1/16756, 8.3KJPN)
A=0.00000 (0/14050, ALFA)
C=0.00000 (0/14050, ALFA)
A=0.0003 (2/6404, 1000G_30x)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
APC2 : 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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 14050 G=1.00000 A=0.00000, C=0.00000
European Sub 9690 G=1.0000 A=0.0000, C=0.0000
African Sub 2898 G=1.0000 A=0.0000, C=0.0000
African Others Sub 114 G=1.000 A=0.000, C=0.000
African American Sub 2784 G=1.0000 A=0.0000, C=0.0000
Asian Sub 112 G=1.000 A=0.000, C=0.000
East Asian Sub 86 G=1.00 A=0.00, C=0.00
Other Asian Sub 26 G=1.00 A=0.00, C=0.00
Latin American 1 Sub 146 G=1.000 A=0.000, C=0.000
Latin American 2 Sub 610 G=1.000 A=0.000, C=0.000
South Asian Sub 98 G=1.00 A=0.00, C=0.00
Other Sub 496 G=1.000 A=0.000, C=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=0.999879 A=0.000121
gnomAD - Exomes Global Study-wide 146810 G=0.999980 A=0.000020
gnomAD - Exomes European Sub 69670 G=1.00000 A=0.00000
gnomAD - Exomes Asian Sub 33796 G=1.00000 A=0.00000
gnomAD - Exomes American Sub 24272 G=0.99996 A=0.00004
gnomAD - Exomes African Sub 7702 G=0.9997 A=0.0003
gnomAD - Exomes Ashkenazi Jewish Sub 7274 G=1.0000 A=0.0000
gnomAD - Exomes Other Sub 4096 G=1.0000 A=0.0000
ExAC Global Study-wide 34110 G=0.99997 A=0.00003
ExAC Europe Sub 19504 G=1.00000 A=0.00000
ExAC Asian Sub 9364 G=1.0000 A=0.0000
ExAC African Sub 2568 G=0.9996 A=0.0004
ExAC American Sub 2464 G=1.0000 A=0.0000
ExAC Other Sub 210 G=1.000 A=0.000
14KJPN JAPANESE Study-wide 28254 G=0.99996 A=0.00004
8.3KJPN JAPANESE Study-wide 16756 G=0.99994 A=0.00006
Allele Frequency Aggregator Total Global 14050 G=1.00000 A=0.00000, C=0.00000
Allele Frequency Aggregator European Sub 9690 G=1.0000 A=0.0000, C=0.0000
Allele Frequency Aggregator African Sub 2898 G=1.0000 A=0.0000, C=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 G=1.000 A=0.000, C=0.000
Allele Frequency Aggregator Other Sub 496 G=1.000 A=0.000, C=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 G=1.000 A=0.000, C=0.000
Allele Frequency Aggregator Asian Sub 112 G=1.000 A=0.000, C=0.000
Allele Frequency Aggregator South Asian Sub 98 G=1.00 A=0.00, C=0.00
1000Genomes_30x Global Study-wide 6404 G=0.9997 A=0.0003
1000Genomes_30x African Sub 1786 G=0.9989 A=0.0011
1000Genomes_30x Europe Sub 1266 G=1.0000 A=0.0000
1000Genomes_30x South Asian Sub 1202 G=1.0000 A=0.0000
1000Genomes_30x East Asian Sub 1170 G=1.0000 A=0.0000
1000Genomes_30x American Sub 980 G=1.000 A=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.1466230G>A
GRCh38.p14 chr 19 NC_000019.10:g.1466230G>C
GRCh37.p13 chr 19 NC_000019.9:g.1466229G>A
GRCh37.p13 chr 19 NC_000019.9:g.1466229G>C
APC2 RefSeqGene NG_055243.1:g.24963G>A
APC2 RefSeqGene NG_055243.1:g.24963G>C
Gene: APC2, APC regulator of WNT signaling pathway 2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
APC2 transcript variant 2 NM_001351273.1:c.2926G>A E [GAG] > K [AAG] Coding Sequence Variant
adenomatous polyposis coli protein 2 isoform 2 NP_001338202.1:p.Glu976Lys E (Glu) > K (Lys) Missense Variant
APC2 transcript variant 2 NM_001351273.1:c.2926G>C E [GAG] > Q [CAG] Coding Sequence Variant
adenomatous polyposis coli protein 2 isoform 2 NP_001338202.1:p.Glu976Gln E (Glu) > Q (Gln) Missense Variant
APC2 transcript variant 1 NM_005883.3:c.2929G>A E [GAG] > K [AAG] Coding Sequence Variant
adenomatous polyposis coli protein 2 isoform 1 NP_005874.1:p.Glu977Lys E (Glu) > K (Lys) Missense Variant
APC2 transcript variant 1 NM_005883.3:c.2929G>C E [GAG] > Q [CAG] Coding Sequence Variant
adenomatous polyposis coli protein 2 isoform 1 NP_005874.1:p.Glu977Gln E (Glu) > Q (Gln) Missense Variant
APC2 transcript variant X1 XM_006722608.4:c.2929G>A E [GAG] > K [AAG] Coding Sequence Variant
adenomatous polyposis coli protein 2 isoform X1 XP_006722671.3:p.Glu977Lys E (Glu) > K (Lys) Missense Variant
APC2 transcript variant X1 XM_006722608.4:c.2929G>C E [GAG] > Q [CAG] Coding Sequence Variant
adenomatous polyposis coli protein 2 isoform X1 XP_006722671.3:p.Glu977Gln E (Glu) > Q (Gln) Missense Variant
APC2 transcript variant X2 XM_006722610.4:c.2926G>A E [GAG] > K [AAG] Coding Sequence Variant
adenomatous polyposis coli protein 2 isoform X2 XP_006722673.3:p.Glu976Lys E (Glu) > K (Lys) Missense Variant
APC2 transcript variant X2 XM_006722610.4:c.2926G>C E [GAG] > Q [CAG] Coding Sequence Variant
adenomatous polyposis coli protein 2 isoform X2 XP_006722673.3:p.Glu976Gln E (Glu) > Q (Gln) Missense Variant
APC2 transcript variant X3 XM_005259475.3:c.3001G>A E [GAG] > K [AAG] Coding Sequence Variant
adenomatous polyposis coli protein 2 isoform X3 XP_005259532.1:p.Glu1001L…

XP_005259532.1:p.Glu1001Lys

 		E (Glu) > K (Lys) Missense Variant
APC2 transcript variant X3 XM_005259475.3:c.3001G>C E [GAG] > Q [CAG] Coding Sequence Variant
adenomatous polyposis coli protein 2 isoform X3 XP_005259532.1:p.Glu1001G…

XP_005259532.1:p.Glu1001Gln

 		E (Glu) > Q (Gln) Missense Variant
APC2 transcript variant X4 XM_006722607.3:c.2998G>A E [GAG] > K [AAG] Coding Sequence Variant
adenomatous polyposis coli protein 2 isoform X4 XP_006722670.1:p.Glu1000L…

XP_006722670.1:p.Glu1000Lys

 		E (Glu) > K (Lys) Missense Variant
APC2 transcript variant X4 XM_006722607.3:c.2998G>C E [GAG] > Q [CAG] Coding Sequence Variant
adenomatous polyposis coli protein 2 isoform X4 XP_006722670.1:p.Glu1000G…

XP_006722670.1:p.Glu1000Gln

 		E (Glu) > Q (Gln) Missense Variant
APC2 transcript variant X5 XM_006722609.4:c.2929G>A E [GAG] > K [AAG] Coding Sequence Variant
adenomatous polyposis coli protein 2 isoform X1 XP_006722672.1:p.Glu977Lys E (Glu) > K (Lys) Missense Variant
APC2 transcript variant X5 XM_006722609.4:c.2929G>C E [GAG] > Q [CAG] Coding Sequence Variant
adenomatous polyposis coli protein 2 isoform X1 XP_006722672.1:p.Glu977Gln E (Glu) > Q (Gln) Missense Variant
APC2 transcript variant X6 XM_047438031.1:c.2926G>A E [GAG] > K [AAG] Coding Sequence Variant
adenomatous polyposis coli protein 2 isoform X2 XP_047293987.1:p.Glu976Lys E (Glu) > K (Lys) Missense Variant
APC2 transcript variant X6 XM_047438031.1:c.2926G>C E [GAG] > Q [CAG] Coding Sequence Variant
adenomatous polyposis coli protein 2 isoform X2 XP_047293987.1:p.Glu976Gln E (Glu) > Q (Gln) Missense Variant
APC2 transcript variant X7 XM_047438032.1:c.2926G>A E [GAG] > K [AAG] Coding Sequence Variant
adenomatous polyposis coli protein 2 isoform X2 XP_047293988.1:p.Glu976Lys E (Glu) > K (Lys) Missense Variant
APC2 transcript variant X7 XM_047438032.1:c.2926G>C E [GAG] > Q [CAG] Coding Sequence Variant
adenomatous polyposis coli protein 2 isoform X2 XP_047293988.1:p.Glu976Gln E (Glu) > Q (Gln) 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 G= A C
GRCh38.p14 chr 19 NC_000019.10:g.1466230= NC_000019.10:g.1466230G>A NC_000019.10:g.1466230G>C
GRCh37.p13 chr 19 NC_000019.9:g.1466229= NC_000019.9:g.1466229G>A NC_000019.9:g.1466229G>C
APC2 RefSeqGene NG_055243.1:g.24963= NG_055243.1:g.24963G>A NG_055243.1:g.24963G>C
APC2 transcript variant 1 NM_005883.3:c.2929= NM_005883.3:c.2929G>A NM_005883.3:c.2929G>C
APC2 transcript variant 1 NM_005883.2:c.2929= NM_005883.2:c.2929G>A NM_005883.2:c.2929G>C
APC2 transcript variant 2 NM_001351273.1:c.2926= NM_001351273.1:c.2926G>A NM_001351273.1:c.2926G>C
APC2 transcript variant X1 XM_006722608.4:c.2929= XM_006722608.4:c.2929G>A XM_006722608.4:c.2929G>C
APC2 transcript variant X1 XM_006722608.3:c.3232= XM_006722608.3:c.3232G>A XM_006722608.3:c.3232G>C
APC2 transcript variant X1 XM_006722608.2:c.2929= XM_006722608.2:c.2929G>A XM_006722608.2:c.2929G>C
APC2 transcript variant X3 XM_006722608.1:c.2929= XM_006722608.1:c.2929G>A XM_006722608.1:c.2929G>C
APC2 transcript variant X2 XM_006722610.4:c.2926= XM_006722610.4:c.2926G>A XM_006722610.4:c.2926G>C
APC2 transcript variant X2 XM_006722610.3:c.3229= XM_006722610.3:c.3229G>A XM_006722610.3:c.3229G>C
APC2 transcript variant X2 XM_006722610.2:c.2926= XM_006722610.2:c.2926G>A XM_006722610.2:c.2926G>C
APC2 transcript variant X5 XM_006722610.1:c.2926= XM_006722610.1:c.2926G>A XM_006722610.1:c.2926G>C
APC2 transcript variant X5 XM_006722609.4:c.2929= XM_006722609.4:c.2929G>A XM_006722609.4:c.2929G>C
APC2 transcript variant X5 XM_006722609.3:c.2929= XM_006722609.3:c.2929G>A XM_006722609.3:c.2929G>C
APC2 transcript variant X5 XM_006722609.2:c.2929= XM_006722609.2:c.2929G>A XM_006722609.2:c.2929G>C
APC2 transcript variant X4 XM_006722609.1:c.2929= XM_006722609.1:c.2929G>A XM_006722609.1:c.2929G>C
APC2 transcript variant X3 XM_005259475.3:c.3001= XM_005259475.3:c.3001G>A XM_005259475.3:c.3001G>C
APC2 transcript variant X3 XM_005259475.2:c.3001= XM_005259475.2:c.3001G>A XM_005259475.2:c.3001G>C
APC2 transcript variant X1 XM_005259475.1:c.3001= XM_005259475.1:c.3001G>A XM_005259475.1:c.3001G>C
APC2 transcript variant X4 XM_006722607.3:c.2998= XM_006722607.3:c.2998G>A XM_006722607.3:c.2998G>C
APC2 transcript variant X4 XM_006722607.2:c.2998= XM_006722607.2:c.2998G>A XM_006722607.2:c.2998G>C
APC2 transcript variant X2 XM_006722607.1:c.2998= XM_006722607.1:c.2998G>A XM_006722607.1:c.2998G>C
APC2 transcript variant X6 XM_047438031.1:c.2926= XM_047438031.1:c.2926G>A XM_047438031.1:c.2926G>C
APC2 transcript variant X7 XM_047438032.1:c.2926= XM_047438032.1:c.2926G>A XM_047438032.1:c.2926G>C
adenomatous polyposis coli protein 2 isoform 1 NP_005874.1:p.Glu977= NP_005874.1:p.Glu977Lys NP_005874.1:p.Glu977Gln
adenomatous polyposis coli protein 2 isoform 2 NP_001338202.1:p.Glu976= NP_001338202.1:p.Glu976Lys NP_001338202.1:p.Glu976Gln
adenomatous polyposis coli protein 2 isoform X1 XP_006722671.3:p.Glu977= XP_006722671.3:p.Glu977Lys XP_006722671.3:p.Glu977Gln
adenomatous polyposis coli protein 2 isoform X2 XP_006722673.3:p.Glu976= XP_006722673.3:p.Glu976Lys XP_006722673.3:p.Glu976Gln
adenomatous polyposis coli protein 2 isoform X1 XP_006722672.1:p.Glu977= XP_006722672.1:p.Glu977Lys XP_006722672.1:p.Glu977Gln
adenomatous polyposis coli protein 2 isoform X3 XP_005259532.1:p.Glu1001= XP_005259532.1:p.Glu1001Lys XP_005259532.1:p.Glu1001Gln
adenomatous polyposis coli protein 2 isoform X4 XP_006722670.1:p.Glu1000= XP_006722670.1:p.Glu1000Lys XP_006722670.1:p.Glu1000Gln
adenomatous polyposis coli protein 2 isoform X2 XP_047293987.1:p.Glu976= XP_047293987.1:p.Glu976Lys XP_047293987.1:p.Glu976Gln
adenomatous polyposis coli protein 2 isoform X2 XP_047293988.1:p.Glu976= XP_047293988.1:p.Glu976Lys XP_047293988.1:p.Glu976Gln
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#.

11 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 EVA_EXAC ss1693229049 Apr 01, 2015 (144)
2 HUMAN_LONGEVITY ss2223678276 Dec 20, 2016 (150)
3 GNOMAD ss2743417670 Nov 08, 2017 (151)
4 GNOMAD ss2749999585 Nov 08, 2017 (151)
5 GNOMAD ss2959562358 Nov 08, 2017 (151)
6 TOPMED ss5065494369 Apr 27, 2021 (155)
7 TOMMO_GENOMICS ss5226342760 Apr 27, 2021 (155)
8 1000G_HIGH_COVERAGE ss5306201009 Oct 16, 2022 (156)
9 EVA ss5512460453 Oct 16, 2022 (156)
10 1000G_HIGH_COVERAGE ss5611488169 Oct 16, 2022 (156)
11 TOMMO_GENOMICS ss5784480880 Oct 16, 2022 (156)
12 1000Genomes_30x NC_000019.10 - 1466230 Oct 16, 2022 (156)
13 ExAC NC_000019.9 - 1466229 Oct 12, 2018 (152)
14 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 531841721 (NC_000019.10:1466229:G:A 21/140270)
Row 531841722 (NC_000019.10:1466229:G:C 0/140270)

- Apr 27, 2021 (155)
15 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 531841721 (NC_000019.10:1466229:G:A 21/140270)
Row 531841722 (NC_000019.10:1466229:G:C 0/140270)

- Apr 27, 2021 (155)
16 gnomAD - Exomes NC_000019.9 - 1466229 Jul 13, 2019 (153)
17 8.3KJPN NC_000019.9 - 1466229 Apr 27, 2021 (155)
18 14KJPN NC_000019.10 - 1466230 Oct 16, 2022 (156)
19 TopMed NC_000019.10 - 1466230 Apr 27, 2021 (155)
20 ALFA NC_000019.10 - 1466230 Apr 27, 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
3706621, 12730859, 84312067, ss1693229049, ss2743417670, ss2749999585, ss2959562358, ss5226342760, ss5512460453 NC_000019.9:1466228:G:A NC_000019.10:1466229:G:A (self)
99014104, 118317984, 281040033, 6126197972, ss2223678276, ss5065494369, ss5306201009, ss5611488169, ss5784480880 NC_000019.10:1466229:G:A NC_000019.10:1466229:G:A (self)
6126197972 NC_000019.10:1466229:G:C NC_000019.10:1466229:G:C (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 rs781574321

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.post761+d5e8e07