Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

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.

rs751991671

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr9:3330457 (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
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.000012 (3/251252, GnomAD_exome)
G=0.000025 (3/121298, ExAC)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
RFX3 : Synonymous Variant
Publications
0 citations
Genomic View
See rs on genome
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
gnomAD - Exomes Global Study-wide 251252 A=0.999988 G=0.000012
gnomAD - Exomes European Sub 135236 A=1.000000 G=0.000000
gnomAD - Exomes Asian Sub 48996 A=0.99994 G=0.00006
gnomAD - Exomes American Sub 34562 A=1.00000 G=0.00000
gnomAD - Exomes African Sub 16254 A=1.00000 G=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10078 A=1.00000 G=0.00000
gnomAD - Exomes Other Sub 6126 A=1.0000 G=0.0000
ExAC Global Study-wide 121298 A=0.999975 G=0.000025
ExAC Europe Sub 73304 A=1.00000 G=0.00000
ExAC Asian Sub 25150 A=0.99988 G=0.00012
ExAC American Sub 11530 A=1.00000 G=0.00000
ExAC African Sub 10406 A=1.00000 G=0.00000
ExAC Other Sub 908 A=1.000 G=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 9 NC_000009.12:g.3330457A>G
GRCh37.p13 chr 9 NC_000009.11:g.3330457A>G
Gene: RFX3, regulatory factor X3 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
RFX3 transcript variant 2 NM_134428.3:c.276T>C N [AAT] > N [AAC] Coding Sequence Variant
transcription factor RFX3 isoform b NP_602304.1:p.Asn92= N (Asn) > N (Asn) Synonymous Variant
RFX3 transcript variant 4 NM_001282117.2:c.276T>C N [AAT] > N [AAC] Coding Sequence Variant
transcription factor RFX3 isoform c NP_001269046.1:p.Asn92= N (Asn) > N (Asn) Synonymous Variant
RFX3 transcript variant 3 NM_001282116.2:c.276T>C N [AAT] > N [AAC] Coding Sequence Variant
transcription factor RFX3 isoform b NP_001269045.1:p.Asn92= N (Asn) > N (Asn) Synonymous Variant
RFX3 transcript variant 5 NM_001377999.1:c.276T>C N [AAT] > N [AAC] Coding Sequence Variant
transcription factor RFX3 isoform d NP_001364928.1:p.Asn92= N (Asn) > N (Asn) Synonymous Variant
RFX3 transcript variant 1 NM_002919.4:c.276T>C N [AAT] > N [AAC] Coding Sequence Variant
transcription factor RFX3 isoform a NP_002910.1:p.Asn92= N (Asn) > N (Asn) Synonymous Variant
RFX3 transcript variant X28 XM_006716847.3:c. N/A Genic Upstream Transcript Variant
RFX3 transcript variant X27 XM_017015002.3:c. N/A Genic Upstream Transcript Variant
RFX3 transcript variant X1 XM_047423687.1:c.366T>C N [AAT] > N [AAC] Coding Sequence Variant
transcription factor RFX3 isoform X1 XP_047279643.1:p.Asn122= N (Asn) > N (Asn) Synonymous Variant
RFX3 transcript variant X2 XM_024447630.2:c.366T>C N [AAT] > N [AAC] Coding Sequence Variant
transcription factor RFX3 isoform X1 XP_024303398.1:p.Asn122= N (Asn) > N (Asn) Synonymous Variant
RFX3 transcript variant X3 XM_047423688.1:c.366T>C N [AAT] > N [AAC] Coding Sequence Variant
transcription factor RFX3 isoform X1 XP_047279644.1:p.Asn122= N (Asn) > N (Asn) Synonymous Variant
RFX3 transcript variant X4 XM_024447631.2:c.366T>C N [AAT] > N [AAC] Coding Sequence Variant
transcription factor RFX3 isoform X1 XP_024303399.1:p.Asn122= N (Asn) > N (Asn) Synonymous Variant
RFX3 transcript variant X5 XM_006716840.3:c.306T>C N [AAT] > N [AAC] Coding Sequence Variant
transcription factor RFX3 isoform X2 XP_006716903.1:p.Asn102= N (Asn) > N (Asn) Synonymous Variant
RFX3 transcript variant X6 XM_047423689.1:c.366T>C N [AAT] > N [AAC] Coding Sequence Variant
transcription factor RFX3 isoform X3 XP_047279645.1:p.Asn122= N (Asn) > N (Asn) Synonymous Variant
RFX3 transcript variant X7 XM_024447632.2:c.294T>C N [AAT] > N [AAC] Coding Sequence Variant
transcription factor RFX3 isoform X4 XP_024303400.1:p.Asn98= N (Asn) > N (Asn) Synonymous Variant
RFX3 transcript variant X8 XM_047423690.1:c.294T>C N [AAT] > N [AAC] Coding Sequence Variant
transcription factor RFX3 isoform X4 XP_047279646.1:p.Asn98= N (Asn) > N (Asn) Synonymous Variant
RFX3 transcript variant X9 XM_047423691.1:c.366T>C N [AAT] > N [AAC] Coding Sequence Variant
transcription factor RFX3 isoform X5 XP_047279647.1:p.Asn122= N (Asn) > N (Asn) Synonymous Variant
RFX3 transcript variant X10 XM_047423692.1:c.276T>C N [AAT] > N [AAC] Coding Sequence Variant
transcription factor RFX3 isoform X6 XP_047279648.1:p.Asn92= N (Asn) > N (Asn) Synonymous Variant
RFX3 transcript variant X11 XM_047423693.1:c.276T>C N [AAT] > N [AAC] Coding Sequence Variant
transcription factor RFX3 isoform X6 XP_047279649.1:p.Asn92= N (Asn) > N (Asn) Synonymous Variant
RFX3 transcript variant X12 XM_047423694.1:c.276T>C N [AAT] > N [AAC] Coding Sequence Variant
transcription factor RFX3 isoform X6 XP_047279650.1:p.Asn92= N (Asn) > N (Asn) Synonymous Variant
RFX3 transcript variant X13 XM_024447634.2:c.276T>C N [AAT] > N [AAC] Coding Sequence Variant
transcription factor RFX3 isoform X6 XP_024303402.1:p.Asn92= N (Asn) > N (Asn) Synonymous Variant
RFX3 transcript variant X14 XM_017015000.3:c.276T>C N [AAT] > N [AAC] Coding Sequence Variant
transcription factor RFX3 isoform X6 XP_016870489.1:p.Asn92= N (Asn) > N (Asn) Synonymous Variant
RFX3 transcript variant X15 XM_006716844.3:c.276T>C N [AAT] > N [AAC] Coding Sequence Variant
transcription factor RFX3 isoform X6 XP_006716907.1:p.Asn92= N (Asn) > N (Asn) Synonymous Variant
RFX3 transcript variant X16 XM_011517998.3:c.276T>C N [AAT] > N [AAC] Coding Sequence Variant
transcription factor RFX3 isoform X6 XP_011516300.1:p.Asn92= N (Asn) > N (Asn) Synonymous Variant
RFX3 transcript variant X17 XM_006716843.3:c.276T>C N [AAT] > N [AAC] Coding Sequence Variant
transcription factor RFX3 isoform X6 XP_006716906.1:p.Asn92= N (Asn) > N (Asn) Synonymous Variant
RFX3 transcript variant X18 XM_024447635.2:c.276T>C N [AAT] > N [AAC] Coding Sequence Variant
transcription factor RFX3 isoform X6 XP_024303403.1:p.Asn92= N (Asn) > N (Asn) Synonymous Variant
RFX3 transcript variant X19 XM_047423695.1:c.306T>C N [AAT] > N [AAC] Coding Sequence Variant
transcription factor RFX3 isoform X7 XP_047279651.1:p.Asn102= N (Asn) > N (Asn) Synonymous Variant
RFX3 transcript variant X20 XM_047423696.1:c.294T>C N [AAT] > N [AAC] Coding Sequence Variant
transcription factor RFX3 isoform X8 XP_047279652.1:p.Asn98= N (Asn) > N (Asn) Synonymous Variant
RFX3 transcript variant X21 XM_047423697.1:c.306T>C N [AAT] > N [AAC] Coding Sequence Variant
transcription factor RFX3 isoform X9 XP_047279653.1:p.Asn102= N (Asn) > N (Asn) Synonymous Variant
RFX3 transcript variant X22 XM_047423698.1:c.366T>C N [AAT] > N [AAC] Coding Sequence Variant
transcription factor RFX3 isoform X10 XP_047279654.1:p.Asn122= N (Asn) > N (Asn) Synonymous Variant
RFX3 transcript variant X23 XM_047423699.1:c.276T>C N [AAT] > N [AAC] Coding Sequence Variant
transcription factor RFX3 isoform X11 XP_047279655.1:p.Asn92= N (Asn) > N (Asn) Synonymous Variant
RFX3 transcript variant X24 XM_047423700.1:c.294T>C N [AAT] > N [AAC] Coding Sequence Variant
transcription factor RFX3 isoform X12 XP_047279656.1:p.Asn98= N (Asn) > N (Asn) Synonymous Variant
RFX3 transcript variant X25 XM_047423701.1:c.276T>C N [AAT] > N [AAC] Coding Sequence Variant
transcription factor RFX3 isoform X13 XP_047279657.1:p.Asn92= N (Asn) > N (Asn) Synonymous Variant
RFX3 transcript variant X26 XM_047423702.1:c.27T>C N [AAT] > N [AAC] Coding Sequence Variant
transcription factor RFX3 isoform X14 XP_047279658.1:p.Asn9= N (Asn) > N (Asn) Synonymous 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 A= G
GRCh38.p14 chr 9 NC_000009.12:g.3330457= NC_000009.12:g.3330457A>G
GRCh37.p13 chr 9 NC_000009.11:g.3330457= NC_000009.11:g.3330457A>G
RFX3 transcript variant 1 NM_002919.4:c.276= NM_002919.4:c.276T>C
RFX3 transcript variant 1 NM_002919.3:c.276= NM_002919.3:c.276T>C
RFX3 transcript variant 1 NM_002919.2:c.276= NM_002919.2:c.276T>C
RFX3 transcript variant X5 XM_006716840.3:c.306= XM_006716840.3:c.306T>C
RFX3 transcript variant X3 XM_006716840.2:c.306= XM_006716840.2:c.306T>C
RFX3 transcript variant X1 XM_006716840.1:c.306= XM_006716840.1:c.306T>C
RFX3 transcript variant X14 XM_017015000.3:c.276= XM_017015000.3:c.276T>C
RFX3 transcript variant X9 XM_017015000.2:c.276= XM_017015000.2:c.276T>C
RFX3 transcript variant X3 XM_017015000.1:c.276= XM_017015000.1:c.276T>C
RFX3 transcript variant X15 XM_006716844.3:c.276= XM_006716844.3:c.276T>C
RFX3 transcript variant X10 XM_006716844.2:c.276= XM_006716844.2:c.276T>C
RFX3 transcript variant X4 XM_006716844.1:c.276= XM_006716844.1:c.276T>C
RFX3 transcript variant 2 NM_134428.3:c.276= NM_134428.3:c.276T>C
RFX3 transcript variant 2 NM_134428.2:c.276= NM_134428.2:c.276T>C
RFX3 transcript variant 2 NM_134428.1:c.276= NM_134428.1:c.276T>C
RFX3 transcript variant X17 XM_006716843.3:c.276= XM_006716843.3:c.276T>C
RFX3 transcript variant X11 XM_006716843.2:c.276= XM_006716843.2:c.276T>C
RFX3 transcript variant X6 XM_006716843.1:c.276= XM_006716843.1:c.276T>C
RFX3 transcript variant X16 XM_011517998.3:c.276= XM_011517998.3:c.276T>C
RFX3 transcript variant X6 XM_011517998.2:c.276= XM_011517998.2:c.276T>C
RFX3 transcript variant X2 XM_011517998.1:c.276= XM_011517998.1:c.276T>C
RFX3 transcript variant X13 XM_024447634.2:c.276= XM_024447634.2:c.276T>C
RFX3 transcript variant X7 XM_024447634.1:c.276= XM_024447634.1:c.276T>C
RFX3 transcript variant X2 XM_024447630.2:c.366= XM_024447630.2:c.366T>C
RFX3 transcript variant X1 XM_024447630.1:c.366= XM_024447630.1:c.366T>C
RFX3 transcript variant X4 XM_024447631.2:c.366= XM_024447631.2:c.366T>C
RFX3 transcript variant X2 XM_024447631.1:c.366= XM_024447631.1:c.366T>C
RFX3 transcript variant X18 XM_024447635.2:c.276= XM_024447635.2:c.276T>C
RFX3 transcript variant X13 XM_024447635.1:c.276= XM_024447635.1:c.276T>C
RFX3 transcript variant X7 XM_024447632.2:c.294= XM_024447632.2:c.294T>C
RFX3 transcript variant X4 XM_024447632.1:c.294= XM_024447632.1:c.294T>C
RFX3 transcript variant 3 NM_001282116.2:c.276= NM_001282116.2:c.276T>C
RFX3 transcript variant 3 NM_001282116.1:c.276= NM_001282116.1:c.276T>C
RFX3 transcript variant 4 NM_001282117.2:c.276= NM_001282117.2:c.276T>C
RFX3 transcript variant 4 NM_001282117.1:c.276= NM_001282117.1:c.276T>C
RFX3 transcript variant X1 XM_047423687.1:c.366= XM_047423687.1:c.366T>C
RFX3 transcript variant X6 XM_047423689.1:c.366= XM_047423689.1:c.366T>C
RFX3 transcript variant X9 XM_047423691.1:c.366= XM_047423691.1:c.366T>C
RFX3 transcript variant X22 XM_047423698.1:c.366= XM_047423698.1:c.366T>C
RFX3 transcript variant X8 XM_047423690.1:c.294= XM_047423690.1:c.294T>C
RFX3 transcript variant X24 XM_047423700.1:c.294= XM_047423700.1:c.294T>C
RFX3 transcript variant X11 XM_047423693.1:c.276= XM_047423693.1:c.276T>C
RFX3 transcript variant X10 XM_047423692.1:c.276= XM_047423692.1:c.276T>C
RFX3 transcript variant X12 XM_047423694.1:c.276= XM_047423694.1:c.276T>C
RFX3 transcript variant X3 XM_047423688.1:c.366= XM_047423688.1:c.366T>C
RFX3 transcript variant X19 XM_047423695.1:c.306= XM_047423695.1:c.306T>C
RFX3 transcript variant X21 XM_047423697.1:c.306= XM_047423697.1:c.306T>C
RFX3 transcript variant X20 XM_047423696.1:c.294= XM_047423696.1:c.294T>C
RFX3 transcript variant 5 NM_001377999.1:c.276= NM_001377999.1:c.276T>C
RFX3 transcript variant X23 XM_047423699.1:c.276= XM_047423699.1:c.276T>C
RFX3 transcript variant X25 XM_047423701.1:c.276= XM_047423701.1:c.276T>C
RFX3 transcript variant X26 XM_047423702.1:c.27= XM_047423702.1:c.27T>C
transcription factor RFX3 isoform a NP_002910.1:p.Asn92= NP_002910.1:p.Asn92=
transcription factor RFX3 isoform X2 XP_006716903.1:p.Asn102= XP_006716903.1:p.Asn102=
transcription factor RFX3 isoform X6 XP_016870489.1:p.Asn92= XP_016870489.1:p.Asn92=
transcription factor RFX3 isoform X6 XP_006716907.1:p.Asn92= XP_006716907.1:p.Asn92=
transcription factor RFX3 isoform b NP_602304.1:p.Asn92= NP_602304.1:p.Asn92=
transcription factor RFX3 isoform X6 XP_006716906.1:p.Asn92= XP_006716906.1:p.Asn92=
transcription factor RFX3 isoform X6 XP_011516300.1:p.Asn92= XP_011516300.1:p.Asn92=
transcription factor RFX3 isoform X6 XP_024303402.1:p.Asn92= XP_024303402.1:p.Asn92=
transcription factor RFX3 isoform X1 XP_024303398.1:p.Asn122= XP_024303398.1:p.Asn122=
transcription factor RFX3 isoform X1 XP_024303399.1:p.Asn122= XP_024303399.1:p.Asn122=
transcription factor RFX3 isoform X6 XP_024303403.1:p.Asn92= XP_024303403.1:p.Asn92=
transcription factor RFX3 isoform X4 XP_024303400.1:p.Asn98= XP_024303400.1:p.Asn98=
transcription factor RFX3 isoform b NP_001269045.1:p.Asn92= NP_001269045.1:p.Asn92=
transcription factor RFX3 isoform c NP_001269046.1:p.Asn92= NP_001269046.1:p.Asn92=
transcription factor RFX3 isoform X1 XP_047279643.1:p.Asn122= XP_047279643.1:p.Asn122=
transcription factor RFX3 isoform X3 XP_047279645.1:p.Asn122= XP_047279645.1:p.Asn122=
transcription factor RFX3 isoform X5 XP_047279647.1:p.Asn122= XP_047279647.1:p.Asn122=
transcription factor RFX3 isoform X10 XP_047279654.1:p.Asn122= XP_047279654.1:p.Asn122=
transcription factor RFX3 isoform X4 XP_047279646.1:p.Asn98= XP_047279646.1:p.Asn98=
transcription factor RFX3 isoform X12 XP_047279656.1:p.Asn98= XP_047279656.1:p.Asn98=
transcription factor RFX3 isoform X6 XP_047279649.1:p.Asn92= XP_047279649.1:p.Asn92=
transcription factor RFX3 isoform X6 XP_047279648.1:p.Asn92= XP_047279648.1:p.Asn92=
transcription factor RFX3 isoform X6 XP_047279650.1:p.Asn92= XP_047279650.1:p.Asn92=
transcription factor RFX3 isoform X1 XP_047279644.1:p.Asn122= XP_047279644.1:p.Asn122=
transcription factor RFX3 isoform X7 XP_047279651.1:p.Asn102= XP_047279651.1:p.Asn102=
transcription factor RFX3 isoform X9 XP_047279653.1:p.Asn102= XP_047279653.1:p.Asn102=
transcription factor RFX3 isoform X8 XP_047279652.1:p.Asn98= XP_047279652.1:p.Asn98=
transcription factor RFX3 isoform d NP_001364928.1:p.Asn92= NP_001364928.1:p.Asn92=
transcription factor RFX3 isoform X11 XP_047279655.1:p.Asn92= XP_047279655.1:p.Asn92=
transcription factor RFX3 isoform X13 XP_047279657.1:p.Asn92= XP_047279657.1:p.Asn92=
transcription factor RFX3 isoform X14 XP_047279658.1:p.Asn9= XP_047279658.1:p.Asn9=
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, 2 Frequency submissions
No Submitter Submission ID Date (Build)
1 EVA_EXAC ss1689402446 Apr 01, 2015 (144)
2 GNOMAD ss2737479248 Nov 08, 2017 (151)
3 ExAC NC_000009.11 - 3330457 Oct 12, 2018 (152)
4 gnomAD - Exomes NC_000009.11 - 3330457 Jul 13, 2019 (153)
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
9518972, 6655929, ss1689402446, ss2737479248 NC_000009.11:3330456:A:G NC_000009.12:3330456:A:G (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 rs751991671

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