Name: rs3135532
Published: September 21, 2022
License: Open Access

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.

rs3135532

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr13:33818157 (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=0.000004 (1/264690, TOPMED)
A=0.000004 (1/243266, GnomAD_exome)
A=0.000007 (1/140312, GnomAD) (+ 3 more)
A=0.000009 (1/113560, ExAC)
A=0.00000 (0/14050, ALFA)
A=0.000 (0/326, HapMap)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: RFC3 : Non Coding Transcript 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
European	Sub	9690	G=1.0000	A=0.0000
African	Sub	2898	G=1.0000	A=0.0000
African Others	Sub	114	G=1.000	A=0.000
African American	Sub	2784	G=1.0000	A=0.0000
Asian	Sub	112	G=1.000	A=0.000
East Asian	Sub	86	G=1.00	A=0.00
Other Asian	Sub	26	G=1.00	A=0.00
Latin American 1	Sub	146	G=1.000	A=0.000
Latin American 2	Sub	610	G=1.000	A=0.000
South Asian	Sub	98	G=1.00	A=0.00
Other	Sub	496	G=1.000	A=0.000

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=0.999996	A=0.000004
gnomAD - Exomes	Global	Study-wide	243266	G=0.999996	A=0.000004
gnomAD - Exomes	European	Sub	131244	G=1.000000	A=0.000000
gnomAD - Exomes	Asian	Sub	48020	G=0.99998	A=0.00002
gnomAD - Exomes	American	Sub	33136	G=1.00000	A=0.00000
gnomAD - Exomes	African	Sub	15214	G=1.00000	A=0.00000
gnomAD - Exomes	Ashkenazi Jewish	Sub	9770	G=1.0000	A=0.0000
gnomAD - Exomes	Other	Sub	5882	G=1.0000	A=0.0000
gnomAD - Genomes	Global	Study-wide	140312	G=0.999993	A=0.000007
gnomAD - Genomes	European	Sub	75972	G=1.00000	A=0.00000
gnomAD - Genomes	African	Sub	42064	G=1.00000	A=0.00000
gnomAD - Genomes	American	Sub	13664	G=1.00000	A=0.00000
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	G=1.0000	A=0.0000
gnomAD - Genomes	East Asian	Sub	3134	G=0.9997	A=0.0003
gnomAD - Genomes	Other	Sub	2154	G=1.0000	A=0.0000
ExAC	Global	Study-wide	113560	G=0.999991	A=0.000009
ExAC	Europe	Sub	67982	G=1.00000	A=0.00000
ExAC	Asian	Sub	24460	G=0.99996	A=0.00004
ExAC	American	Sub	11268	G=1.00000	A=0.00000
ExAC	African	Sub	9002	G=1.0000	A=0.0000
ExAC	Other	Sub	848	G=1.000	A=0.000
Allele Frequency Aggregator	Total	Global	14050	G=1.00000	A=0.00000
Allele Frequency Aggregator	European	Sub	9690	G=1.0000	A=0.0000
Allele Frequency Aggregator	African	Sub	2898	G=1.0000	A=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	610	G=1.000	A=0.000
Allele Frequency Aggregator	Other	Sub	496	G=1.000	A=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	G=1.000	A=0.000
Allele Frequency Aggregator	Asian	Sub	112	G=1.000	A=0.000
Allele Frequency Aggregator	South Asian	Sub	98	G=1.00	A=0.00
HapMap	Global	Study-wide	326	G=1.000	A=0.000
HapMap	American	Sub	120	G=1.000	A=0.000
HapMap	African	Sub	116	G=1.000	A=0.000
HapMap	Asian	Sub	90	G=1.00	A=0.00

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 13	NC_000013.11:g.33818157G>A
GRCh38.p14 chr 13	NC_000013.11:g.33818157G>C
GRCh37.p13 chr 13	NC_000013.10:g.34392294G>A
GRCh37.p13 chr 13	NC_000013.10:g.34392294G>C

Gene: RFC3, replication factor C subunit 3 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
RFC3 transcript variant 1	NM_002915.4:c.-22=	N/A	5 Prime UTR Variant
RFC3 transcript variant 2	NM_181558.3:c.-22=	N/A	5 Prime UTR Variant
RFC3 transcript variant X1	XM_011535172.4:c.-22=	N/A	5 Prime UTR Variant
RFC3 transcript variant X2	XM_017020680.3:c.-22=	N/A	5 Prime UTR Variant
RFC3 transcript variant X3	XM_047430489.1:c.-22=	N/A	5 Prime UTR Variant
RFC3 transcript variant X12	XM_047430490.1:c.-22=	N/A	5 Prime UTR Variant
RFC3 transcript variant X4	XM_047430491.1:c.-22=	N/A	5 Prime UTR Variant
RFC3 transcript variant X5	XM_011535173.4:c.-22=	N/A	5 Prime UTR Variant
RFC3 transcript variant X6	XM_011535175.3:c.-22=	N/A	5 Prime UTR Variant
RFC3 transcript variant X7	XM_017020681.3:c.-22=	N/A	5 Prime UTR Variant
RFC3 transcript variant X8	XM_017020682.3:c.-22=	N/A	5 Prime UTR Variant
RFC3 transcript variant X9	XM_047430492.1:c.-22=	N/A	5 Prime UTR Variant
RFC3 transcript variant X10	XM_017020683.3:c.-22=	N/A	5 Prime UTR Variant
RFC3 transcript variant X11	XR_007063695.1:n.9G>A	N/A	Non Coding Transcript Variant
RFC3 transcript variant X11	XR_007063695.1:n.9G>C	N/A	Non Coding Transcript Variant

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

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 13	NC_000013.11:g.33818157=	NC_000013.11:g.33818157G>A	NC_000013.11:g.33818157G>C
GRCh37.p13 chr 13	NC_000013.10:g.34392294=	NC_000013.10:g.34392294G>A	NC_000013.10:g.34392294G>C
RFC3 transcript variant X1	XM_011535172.4:c.-22=	XM_011535172.4:c.-22G>A	XM_011535172.4:c.-22G>C
RFC3 transcript variant X1	XM_011535172.3:c.-22=	XM_011535172.3:c.-22G>A	XM_011535172.3:c.-22G>C
RFC3 transcript variant X1	XM_011535172.2:c.-22=	XM_011535172.2:c.-22G>A	XM_011535172.2:c.-22G>C
RFC3 transcript variant X1	XM_011535172.1:c.-22=	XM_011535172.1:c.-22G>A	XM_011535172.1:c.-22G>C
RFC3 transcript variant X5	XM_011535173.4:c.-22=	XM_011535173.4:c.-22G>A	XM_011535173.4:c.-22G>C
RFC3 transcript variant X3	XM_011535173.3:c.-22=	XM_011535173.3:c.-22G>A	XM_011535173.3:c.-22G>C
RFC3 transcript variant X3	XM_011535173.2:c.-22=	XM_011535173.2:c.-22G>A	XM_011535173.2:c.-22G>C
RFC3 transcript variant X2	XM_011535173.1:c.-22=	XM_011535173.1:c.-22G>A	XM_011535173.1:c.-22G>C
RFC3 transcript variant 1	NM_002915.4:c.-22=	NM_002915.4:c.-22G>A	NM_002915.4:c.-22G>C
RFC3 transcript variant 1	NM_002915.3:c.-22=	NM_002915.3:c.-22G>A	NM_002915.3:c.-22G>C
RFC3 transcript variant X2	XM_017020680.3:c.-22=	XM_017020680.3:c.-22G>A	XM_017020680.3:c.-22G>C
RFC3 transcript variant X2	XM_017020680.2:c.-22=	XM_017020680.2:c.-22G>A	XM_017020680.2:c.-22G>C
RFC3 transcript variant X2	XM_017020680.1:c.-22=	XM_017020680.1:c.-22G>A	XM_017020680.1:c.-22G>C
RFC3 transcript variant X8	XM_017020682.3:c.-22=	XM_017020682.3:c.-22G>A	XM_017020682.3:c.-22G>C
RFC3 transcript variant X7	XM_017020682.2:c.-22=	XM_017020682.2:c.-22G>A	XM_017020682.2:c.-22G>C
RFC3 transcript variant X7	XM_017020682.1:c.-22=	XM_017020682.1:c.-22G>A	XM_017020682.1:c.-22G>C
RFC3 transcript variant X6	XM_011535175.3:c.-22=	XM_011535175.3:c.-22G>A	XM_011535175.3:c.-22G>C
RFC3 transcript variant X6	XM_011535175.2:c.-22=	XM_011535175.2:c.-22G>A	XM_011535175.2:c.-22G>C
RFC3 transcript variant X6	XM_011535175.1:c.-22=	XM_011535175.1:c.-22G>A	XM_011535175.1:c.-22G>C
RFC3 transcript variant 2	NM_181558.3:c.-22=	NM_181558.3:c.-22G>A	NM_181558.3:c.-22G>C
RFC3 transcript variant 2	NM_181558.2:c.-22=	NM_181558.2:c.-22G>A	NM_181558.2:c.-22G>C
RFC3 transcript variant X10	XM_017020683.3:c.-22=	XM_017020683.3:c.-22G>A	XM_017020683.3:c.-22G>C
RFC3 transcript variant X8	XM_017020683.2:c.-22=	XM_017020683.2:c.-22G>A	XM_017020683.2:c.-22G>C
RFC3 transcript variant X8	XM_017020683.1:c.-22=	XM_017020683.1:c.-22G>A	XM_017020683.1:c.-22G>C
RFC3 transcript variant X7	XM_017020681.3:c.-22=	XM_017020681.3:c.-22G>A	XM_017020681.3:c.-22G>C
RFC3 transcript variant X4	XM_017020681.2:c.-22=	XM_017020681.2:c.-22G>A	XM_017020681.2:c.-22G>C
RFC3 transcript variant X4	XM_017020681.1:c.-22=	XM_017020681.1:c.-22G>A	XM_017020681.1:c.-22G>C
RFC3 transcript variant X3	XM_047430489.1:c.-22=	XM_047430489.1:c.-22G>A	XM_047430489.1:c.-22G>C
RFC3 transcript variant X12	XM_047430490.1:c.-22=	XM_047430490.1:c.-22G>A	XM_047430490.1:c.-22G>C
RFC3 transcript variant X11	XR_007063695.1:n.9=	XR_007063695.1:n.9G>A	XR_007063695.1:n.9G>C
RFC3 transcript variant X4	XM_047430491.1:c.-22=	XM_047430491.1:c.-22G>A	XM_047430491.1:c.-22G>C
RFC3 transcript variant X9	XM_047430492.1:c.-22=	XM_047430492.1:c.-22G>A	XM_047430492.1:c.-22G>C

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#.

6 SubSNP, 6 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	EGP_SNPS	ss4383625	Mar 26, 2002 (103)
2	EVA_EXAC	ss1691256123	Apr 01, 2015 (144)
3	HUMAN_LONGEVITY	ss2195412392	Dec 20, 2016 (150)
4	GNOMAD	ss4263891366	Apr 27, 2021 (155)
5	TOPMED	ss4942299054	Apr 27, 2021 (155)
6	EVA	ss5850677941	Oct 16, 2022 (156)
7	ExAC	NC_000013.10 - 34392294	Oct 12, 2018 (152)
8	gnomAD - Genomes	NC_000013.11 - 33818157	Apr 27, 2021 (155)
9	gnomAD - Exomes	NC_000013.10 - 34392294	Jul 13, 2019 (153)
10	HapMap	NC_000013.11 - 33818157	Apr 27, 2020 (154)
11	TopMed	NC_000013.11 - 33818157	Apr 27, 2021 (155)
12	ALFA	NC_000013.11 - 33818157	Apr 27, 2021 (155)

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
1582276, 9604157, ss1691256123	NC_000013.10:34392293:G:A	NC_000013.11:33818156:G:A	(self)
427456193, 964590, 157844712, 10102370701, ss2195412392, ss4263891366, ss4942299054, ss5850677941	NC_000013.11:33818156:G:A	NC_000013.11:33818156:G:A	(self)
ss4383625	NT_024524.14:15372293:G:A	NC_000013.11:33818156:G:A	(self)
ss2195412392	NC_000013.11:33818156:G:C	NC_000013.11:33818156:G:C	(self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs3135532

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs3135532