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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.

rs773534874

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr19:42117396 (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=0.000049 (13/264690, TOPMED)
A=0.000005 (1/189538, GnomAD_exome)
A=0.000036 (5/139982, GnomAD) (+ 2 more)
A=0.000009 (1/117360, ExAC)
A=0.00000 (0/14050, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
POU2F2 : 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 C=1.00000 A=0.00000
European Sub 9690 C=1.0000 A=0.0000
African Sub 2898 C=1.0000 A=0.0000
African Others Sub 114 C=1.000 A=0.000
African American Sub 2784 C=1.0000 A=0.0000
Asian Sub 112 C=1.000 A=0.000
East Asian Sub 86 C=1.00 A=0.00
Other Asian Sub 26 C=1.00 A=0.00
Latin American 1 Sub 146 C=1.000 A=0.000
Latin American 2 Sub 610 C=1.000 A=0.000
South Asian Sub 98 C=1.00 A=0.00
Other Sub 496 C=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 C=0.999951 A=0.000049
gnomAD - Exomes Global Study-wide 189538 C=0.999995 A=0.000005
gnomAD - Exomes European Sub 111432 C=1.000000 A=0.000000
gnomAD - Exomes Asian Sub 34680 C=1.00000 A=0.00000
gnomAD - Exomes American Sub 20212 C=1.00000 A=0.00000
gnomAD - Exomes African Sub 11334 C=0.99991 A=0.00009
gnomAD - Exomes Ashkenazi Jewish Sub 7522 C=1.0000 A=0.0000
gnomAD - Exomes Other Sub 4358 C=1.0000 A=0.0000
gnomAD - Genomes Global Study-wide 139982 C=0.999964 A=0.000036
gnomAD - Genomes European Sub 75848 C=1.00000 A=0.00000
gnomAD - Genomes African Sub 41924 C=0.99988 A=0.00012
gnomAD - Genomes American Sub 13622 C=1.00000 A=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3324 C=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3124 C=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2140 C=1.0000 A=0.0000
ExAC Global Study-wide 117360 C=0.999991 A=0.000009
ExAC Europe Sub 71040 C=1.00000 A=0.00000
ExAC Asian Sub 24954 C=1.00000 A=0.00000
ExAC American Sub 11490 C=1.00000 A=0.00000
ExAC African Sub 8996 C=0.9999 A=0.0001
ExAC Other Sub 880 C=1.000 A=0.000
Allele Frequency Aggregator Total Global 14050 C=1.00000 A=0.00000
Allele Frequency Aggregator European Sub 9690 C=1.0000 A=0.0000
Allele Frequency Aggregator African Sub 2898 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 496 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 112 C=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 98 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 19 NC_000019.10:g.42117396C>A
GRCh37.p13 chr 19 NC_000019.9:g.42621548C>A
POU2F2 RefSeqGene NG_030365.1:g.20078G>T
Gene: POU2F2, POU class 2 homeobox 2 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
POU2F2 transcript variant 1 NM_001207025.4:c.187-30G>T N/A Intron Variant
POU2F2 transcript variant 3 NM_001207026.3:c.187-30G>T N/A Intron Variant
POU2F2 transcript variant 4 NM_001247994.3:c.187-30G>T N/A Intron Variant
POU2F2 transcript variant 7 NM_001393936.1:c.187-30G>T N/A Intron Variant
POU2F2 transcript variant 9 NM_001394377.1:c.187-30G>T N/A Intron Variant
POU2F2 transcript variant 10 NM_001394378.1:c.187-30G>T N/A Intron Variant
POU2F2 transcript variant 2 NM_002698.6:c.187-30G>T N/A Intron Variant
POU2F2 transcript variant 6 NM_001393935.1:c.223G>T G [GGT] > C [TGT] Coding Sequence Variant
POU domain, class 2, transcription factor 2 isoform 6 NP_001380864.1:p.Gly75Cys G (Gly) > C (Cys) Missense Variant
POU2F2 transcript variant 5 NM_001393934.1:c.187G>T G [GGT] > C [TGT] Coding Sequence Variant
POU domain, class 2, transcription factor 2 isoform 5 NP_001380863.1:p.Gly63Cys G (Gly) > C (Cys) Missense Variant
POU2F2 transcript variant 8 NM_001394376.1:c.223G>T G [GGT] > C [TGT] Coding Sequence Variant
POU domain, class 2, transcription factor 2 isoform 8 NP_001381305.1:p.Gly75Cys G (Gly) > C (Cys) Missense Variant
POU2F2 transcript variant X3 XM_017026892.3:c.187-30G>T N/A Intron Variant
POU2F2 transcript variant X15 XM_017026894.3:c.187-30G>T N/A Intron Variant
POU2F2 transcript variant X1 XM_047438953.1:c.187-30G>T N/A Intron Variant
POU2F2 transcript variant X7 XM_047438957.1:c.187-30G>T N/A Intron Variant
POU2F2 transcript variant X10 XM_047438960.1:c.187-30G>T N/A Intron Variant
POU2F2 transcript variant X11 XM_047438961.1:c.151-30G>T N/A Intron Variant
POU2F2 transcript variant X12 XM_047438962.1:c.151-30G>T N/A Intron Variant
POU2F2 transcript variant X13 XM_047438963.1:c.187-30G>T N/A Intron Variant
POU2F2 transcript variant X14 XM_047438964.1:c.187-30G>T N/A Intron Variant
POU2F2 transcript variant X17 XM_047438966.1:c.151-30G>T N/A Intron Variant
POU2F2 transcript variant X21 XM_047438968.1:c. N/A Genic Upstream Transcript Variant
POU2F2 transcript variant X2 XM_017026891.3:c.223G>T G [GGT] > C [TGT] Coding Sequence Variant
POU domain, class 2, transcription factor 2 isoform X2 XP_016882380.1:p.Gly75Cys G (Gly) > C (Cys) Missense Variant
POU2F2 transcript variant X4 XM_047438954.1:c.187G>T G [GGT] > C [TGT] Coding Sequence Variant
POU domain, class 2, transcription factor 2 isoform X4 XP_047294910.1:p.Gly63Cys G (Gly) > C (Cys) Missense Variant
POU2F2 transcript variant X5 XM_047438955.1:c.187G>T G [GGT] > C [TGT] Coding Sequence Variant
POU domain, class 2, transcription factor 2 isoform X4 XP_047294911.1:p.Gly63Cys G (Gly) > C (Cys) Missense Variant
POU2F2 transcript variant X6 XM_047438956.1:c.187G>T G [GGT] > C [TGT] Coding Sequence Variant
POU domain, class 2, transcription factor 2 isoform X4 XP_047294912.1:p.Gly63Cys G (Gly) > C (Cys) Missense Variant
POU2F2 transcript variant X8 XM_047438958.1:c.223G>T G [GGT] > C [TGT] Coding Sequence Variant
POU domain, class 2, transcription factor 2 isoform X6 XP_047294914.1:p.Gly75Cys G (Gly) > C (Cys) Missense Variant
POU2F2 transcript variant X9 XM_047438959.1:c.223G>T G [GGT] > C [TGT] Coding Sequence Variant
POU domain, class 2, transcription factor 2 isoform X7 XP_047294915.1:p.Gly75Cys G (Gly) > C (Cys) Missense Variant
POU2F2 transcript variant X16 XM_047438965.1:c.187G>T G [GGT] > C [TGT] Coding Sequence Variant
POU domain, class 2, transcription factor 2 isoform X13 XP_047294921.1:p.Gly63Cys G (Gly) > C (Cys) Missense Variant
POU2F2 transcript variant X18 XM_011527041.4:c.223G>T G [GGT] > C [TGT] Coding Sequence Variant
POU domain, class 2, transcription factor 2 isoform X15 XP_011525343.1:p.Gly75Cys G (Gly) > C (Cys) Missense Variant
POU2F2 transcript variant X19 XM_011527042.4:c.223G>T G [GGT] > C [TGT] Coding Sequence Variant
POU domain, class 2, transcription factor 2 isoform X16 XP_011525344.1:p.Gly75Cys G (Gly) > C (Cys) Missense Variant
POU2F2 transcript variant X20 XM_047438967.1:c.223G>T G [GGT] > C [TGT] Coding Sequence Variant
POU domain, class 2, transcription factor 2 isoform X17 XP_047294923.1:p.Gly75Cys G (Gly) > C (Cys) 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= A
GRCh38.p14 chr 19 NC_000019.10:g.42117396= NC_000019.10:g.42117396C>A
GRCh37.p13 chr 19 NC_000019.9:g.42621548= NC_000019.9:g.42621548C>A
POU2F2 RefSeqGene NG_030365.1:g.20078= NG_030365.1:g.20078G>T
POU2F2 transcript variant 5 NM_001393934.1:c.187= NM_001393934.1:c.187G>T
POU2F2 transcript variant 8 NM_001394376.1:c.223= NM_001394376.1:c.223G>T
POU2F2 transcript variant 6 NM_001393935.1:c.223= NM_001393935.1:c.223G>T
POU2F2 transcript variant X18 XM_011527041.4:c.223= XM_011527041.4:c.223G>T
POU2F2 transcript variant X21 XM_011527041.3:c.223= XM_011527041.3:c.223G>T
POU2F2 transcript variant X18 XM_011527041.2:c.223= XM_011527041.2:c.223G>T
POU2F2 transcript variant X3 XM_011527041.1:c.223= XM_011527041.1:c.223G>T
POU2F2 transcript variant X19 XM_011527042.4:c.223= XM_011527042.4:c.223G>T
POU2F2 transcript variant X22 XM_011527042.3:c.223= XM_011527042.3:c.223G>T
POU2F2 transcript variant X19 XM_011527042.2:c.223= XM_011527042.2:c.223G>T
POU2F2 transcript variant X4 XM_011527042.1:c.223= XM_011527042.1:c.223G>T
POU2F2 transcript variant X2 XM_017026891.3:c.223= XM_017026891.3:c.223G>T
POU2F2 transcript variant X8 XM_017026891.2:c.223= XM_017026891.2:c.223G>T
POU2F2 transcript variant X8 XM_017026891.1:c.223= XM_017026891.1:c.223G>T
POU2F2 transcript variant X4 XM_047438954.1:c.187= XM_047438954.1:c.187G>T
POU2F2 transcript variant X5 XM_047438955.1:c.187= XM_047438955.1:c.187G>T
POU2F2 transcript variant X9 XM_047438959.1:c.223= XM_047438959.1:c.223G>T
POU2F2 transcript variant X8 XM_047438958.1:c.223= XM_047438958.1:c.223G>T
POU2F2 transcript variant X6 XM_047438956.1:c.187= XM_047438956.1:c.187G>T
POU2F2 transcript variant X16 XM_047438965.1:c.187= XM_047438965.1:c.187G>T
POU2F2 transcript variant X20 XM_047438967.1:c.223= XM_047438967.1:c.223G>T
POU domain, class 2, transcription factor 2 isoform 5 NP_001380863.1:p.Gly63= NP_001380863.1:p.Gly63Cys
POU domain, class 2, transcription factor 2 isoform 8 NP_001381305.1:p.Gly75= NP_001381305.1:p.Gly75Cys
POU domain, class 2, transcription factor 2 isoform 6 NP_001380864.1:p.Gly75= NP_001380864.1:p.Gly75Cys
POU domain, class 2, transcription factor 2 isoform X15 XP_011525343.1:p.Gly75= XP_011525343.1:p.Gly75Cys
POU domain, class 2, transcription factor 2 isoform X16 XP_011525344.1:p.Gly75= XP_011525344.1:p.Gly75Cys
POU domain, class 2, transcription factor 2 isoform X2 XP_016882380.1:p.Gly75= XP_016882380.1:p.Gly75Cys
POU domain, class 2, transcription factor 2 isoform X4 XP_047294910.1:p.Gly63= XP_047294910.1:p.Gly63Cys
POU domain, class 2, transcription factor 2 isoform X4 XP_047294911.1:p.Gly63= XP_047294911.1:p.Gly63Cys
POU domain, class 2, transcription factor 2 isoform X7 XP_047294915.1:p.Gly75= XP_047294915.1:p.Gly75Cys
POU domain, class 2, transcription factor 2 isoform X6 XP_047294914.1:p.Gly75= XP_047294914.1:p.Gly75Cys
POU domain, class 2, transcription factor 2 isoform X4 XP_047294912.1:p.Gly63= XP_047294912.1:p.Gly63Cys
POU domain, class 2, transcription factor 2 isoform X13 XP_047294921.1:p.Gly63= XP_047294921.1:p.Gly63Cys
POU domain, class 2, transcription factor 2 isoform X17 XP_047294923.1:p.Gly75= XP_047294923.1:p.Gly75Cys
POU2F2 transcript variant 1 NM_001207025.2:c.187-30= NM_001207025.2:c.187-30G>T
POU2F2 transcript variant 1 NM_001207025.4:c.187-30= NM_001207025.4:c.187-30G>T
POU2F2 transcript variant 3 NM_001207026.1:c.187-30= NM_001207026.1:c.187-30G>T
POU2F2 transcript variant 3 NM_001207026.3:c.187-30= NM_001207026.3:c.187-30G>T
POU2F2 transcript variant 4 NM_001247994.1:c.187-30= NM_001247994.1:c.187-30G>T
POU2F2 transcript variant 4 NM_001247994.3:c.187-30= NM_001247994.3:c.187-30G>T
POU2F2 transcript variant 7 NM_001393936.1:c.187-30= NM_001393936.1:c.187-30G>T
POU2F2 transcript variant 9 NM_001394377.1:c.187-30= NM_001394377.1:c.187-30G>T
POU2F2 transcript variant 10 NM_001394378.1:c.187-30= NM_001394378.1:c.187-30G>T
POU2F2 transcript variant 2 NM_002698.4:c.187-30= NM_002698.4:c.187-30G>T
POU2F2 transcript variant 2 NM_002698.6:c.187-30= NM_002698.6:c.187-30G>T
POU2F2 transcript variant X1 XM_005259009.1:c.187-30= XM_005259009.1:c.187-30G>T
POU2F2 transcript variant X2 XM_005259010.1:c.187-30= XM_005259010.1:c.187-30G>T
POU2F2 transcript variant X3 XM_005259011.1:c.187-30= XM_005259011.1:c.187-30G>T
POU2F2 transcript variant X4 XM_005259012.1:c.187-30= XM_005259012.1:c.187-30G>T
POU2F2 transcript variant X3 XM_017026892.3:c.187-30= XM_017026892.3:c.187-30G>T
POU2F2 transcript variant X15 XM_017026894.3:c.187-30= XM_017026894.3:c.187-30G>T
POU2F2 transcript variant X1 XM_047438953.1:c.187-30= XM_047438953.1:c.187-30G>T
POU2F2 transcript variant X7 XM_047438957.1:c.187-30= XM_047438957.1:c.187-30G>T
POU2F2 transcript variant X10 XM_047438960.1:c.187-30= XM_047438960.1:c.187-30G>T
POU2F2 transcript variant X11 XM_047438961.1:c.151-30= XM_047438961.1:c.151-30G>T
POU2F2 transcript variant X12 XM_047438962.1:c.151-30= XM_047438962.1:c.151-30G>T
POU2F2 transcript variant X13 XM_047438963.1:c.187-30= XM_047438963.1:c.187-30G>T
POU2F2 transcript variant X14 XM_047438964.1:c.187-30= XM_047438964.1:c.187-30G>T
POU2F2 transcript variant X17 XM_047438966.1:c.151-30= XM_047438966.1:c.151-30G>T
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#.

4 SubSNP, 5 Frequency submissions
No Submitter Submission ID Date (Build)
1 EVA_EXAC ss1693631264 Apr 01, 2015 (144)
2 GNOMAD ss2744039746 Nov 08, 2017 (151)
3 GNOMAD ss4331579218 Apr 26, 2021 (155)
4 TOPMED ss5075424771 Apr 26, 2021 (155)
5 ExAC NC_000019.9 - 42621548 Oct 12, 2018 (152)
6 gnomAD - Genomes NC_000019.10 - 42117396 Apr 26, 2021 (155)
7 gnomAD - Exomes NC_000019.9 - 42621548 Jul 13, 2019 (153)
8 TopMed NC_000019.10 - 42117396 Apr 26, 2021 (155)
9 ALFA NC_000019.10 - 42117396 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
4137678, 13353663, ss1693631264, ss2744039746 NC_000019.9:42621547:C:A NC_000019.10:42117395:C:A (self)
540561634, 290970435, 13046684162, ss4331579218, ss5075424771 NC_000019.10:42117395:C:A NC_000019.10:42117395: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 rs773534874

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