Name: rs542810776
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.

rs542810776

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr2:25742033 (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 / C>G / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.000008 (2/246796, GnomAD_exome)
T=0.000007 (1/140238, GnomAD)
A=0.000009 (1/115922, ExAC) (+ 5 more)
T=0.00004 (3/78696, PAGE_STUDY)
G=0.00000 (0/14710, ALFA)
T=0.00000 (0/14710, ALFA)
A=0.0002 (1/6404, 1000G_30x)
A=0.0002 (1/5008, 1000G)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ASXL2 : 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	14710	C=1.00000	G=0.00000, T=0.00000
European	Sub	9768	C=1.0000	G=0.0000, T=0.0000
African	Sub	3332	C=1.0000	G=0.0000, T=0.0000
African Others	Sub	114	C=1.000	G=0.000, T=0.000
African American	Sub	3218	C=1.0000	G=0.0000, T=0.0000
Asian	Sub	146	C=1.000	G=0.000, T=0.000
East Asian	Sub	120	C=1.000	G=0.000, T=0.000
Other Asian	Sub	26	C=1.00	G=0.00, T=0.00
Latin American 1	Sub	146	C=1.000	G=0.000, T=0.000
Latin American 2	Sub	610	C=1.000	G=0.000, T=0.000
South Asian	Sub	104	C=1.000	G=0.000, T=0.000
Other	Sub	604	C=1.000	G=0.000, T=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").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
gnomAD - Exomes	Global	Study-wide	246796	C=0.999992	T=0.000008
gnomAD - Exomes	European	Sub	133122	C=0.999992	T=0.000008
gnomAD - Exomes	Asian	Sub	48022	C=1.00000	T=0.00000
gnomAD - Exomes	American	Sub	34388	C=1.00000	T=0.00000
gnomAD - Exomes	African	Sub	15480	C=0.99994	T=0.00006
gnomAD - Exomes	Ashkenazi Jewish	Sub	9800	C=1.0000	T=0.0000
gnomAD - Exomes	Other	Sub	5984	C=1.0000	T=0.0000
gnomAD - Genomes	Global	Study-wide	140238	C=0.999993	T=0.000007
gnomAD - Genomes	European	Sub	75944	C=0.99999	T=0.00001
gnomAD - Genomes	African	Sub	42030	C=1.00000	T=0.00000
gnomAD - Genomes	American	Sub	13658	C=1.00000	T=0.00000
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	C=1.0000	T=0.0000
gnomAD - Genomes	East Asian	Sub	3134	C=1.0000	T=0.0000
gnomAD - Genomes	Other	Sub	2148	C=1.0000	T=0.0000
ExAC	Global	Study-wide	115922	C=0.999991	A=0.000009
ExAC	Europe	Sub	72020	C=1.00000	A=0.00000
ExAC	Asian	Sub	21782	C=1.00000	A=0.00000
ExAC	American	Sub	11536	C=0.99991	A=0.00009
ExAC	African	Sub	9746	C=1.0000	A=0.0000
ExAC	Other	Sub	838	C=1.000	A=0.000
The PAGE Study	Global	Study-wide	78696	C=0.99996	T=0.00004
The PAGE Study	AfricanAmerican	Sub	32514	C=0.99994	T=0.00006
The PAGE Study	Mexican	Sub	10808	C=1.00000	T=0.00000
The PAGE Study	Asian	Sub	8316	C=1.0000	T=0.0000
The PAGE Study	PuertoRican	Sub	7918	C=1.0000	T=0.0000
The PAGE Study	NativeHawaiian	Sub	4534	C=1.0000	T=0.0000
The PAGE Study	Cuban	Sub	4230	C=1.0000	T=0.0000
The PAGE Study	Dominican	Sub	3828	C=0.9997	T=0.0003
The PAGE Study	CentralAmerican	Sub	2450	C=1.0000	T=0.0000
The PAGE Study	SouthAmerican	Sub	1982	C=1.0000	T=0.0000
The PAGE Study	NativeAmerican	Sub	1260	C=1.0000	T=0.0000
The PAGE Study	SouthAsian	Sub	856	C=1.000	T=0.000
Allele Frequency Aggregator	Total	Global	14710	C=1.00000	G=0.00000, T=0.00000
Allele Frequency Aggregator	European	Sub	9768	C=1.0000	G=0.0000, T=0.0000
Allele Frequency Aggregator	African	Sub	3332	C=1.0000	G=0.0000, T=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	610	C=1.000	G=0.000, T=0.000
Allele Frequency Aggregator	Other	Sub	604	C=1.000	G=0.000, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	C=1.000	G=0.000, T=0.000
Allele Frequency Aggregator	Asian	Sub	146	C=1.000	G=0.000, T=0.000
Allele Frequency Aggregator	South Asian	Sub	104	C=1.000	G=0.000, T=0.000
1000Genomes_30x	Global	Study-wide	6404	C=0.9998	A=0.0002
1000Genomes_30x	African	Sub	1786	C=1.0000	A=0.0000
1000Genomes_30x	Europe	Sub	1266	C=1.0000	A=0.0000
1000Genomes_30x	South Asian	Sub	1202	C=1.0000	A=0.0000
1000Genomes_30x	East Asian	Sub	1170	C=1.0000	A=0.0000
1000Genomes_30x	American	Sub	980	C=0.999	A=0.001
1000Genomes	Global	Study-wide	5008	C=0.9998	A=0.0002
1000Genomes	African	Sub	1322	C=1.0000	A=0.0000
1000Genomes	East Asian	Sub	1008	C=1.0000	A=0.0000
1000Genomes	Europe	Sub	1006	C=1.0000	A=0.0000
1000Genomes	South Asian	Sub	978	C=1.000	A=0.000
1000Genomes	American	Sub	694	C=0.999	A=0.001

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 2	NC_000002.12:g.25742033C>A
GRCh38.p14 chr 2	NC_000002.12:g.25742033C>G
GRCh38.p14 chr 2	NC_000002.12:g.25742033C>T
GRCh37.p13 chr 2	NC_000002.11:g.25964902C>A
GRCh37.p13 chr 2	NC_000002.11:g.25964902C>G
GRCh37.p13 chr 2	NC_000002.11:g.25964902C>T
ASXL2 RefSeqGene (LRG_1421)	NG_052995.1:g.141484G>T
ASXL2 RefSeqGene (LRG_1421)	NG_052995.1:g.141484G>C
ASXL2 RefSeqGene (LRG_1421)	NG_052995.1:g.141484G>A

Gene: ASXL2, ASXL transcriptional regulator 2 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ASXL2 transcript variant 1	NM_018263.6:c.4304G>T	R [CGG] > L [CTG]	Coding Sequence Variant
putative Polycomb group protein ASXL2 isoform 1	NP_060733.4:p.Arg1435Leu	R (Arg) > L (Leu)	Missense Variant
ASXL2 transcript variant 1	NM_018263.6:c.4304G>C	R [CGG] > P [CCG]	Coding Sequence Variant
putative Polycomb group protein ASXL2 isoform 1	NP_060733.4:p.Arg1435Pro	R (Arg) > P (Pro)	Missense Variant
ASXL2 transcript variant 1	NM_018263.6:c.4304G>A	R [CGG] > Q [CAG]	Coding Sequence Variant
putative Polycomb group protein ASXL2 isoform 1	NP_060733.4:p.Arg1435Gln	R (Arg) > Q (Gln)	Missense Variant
ASXL2 transcript variant 3	NM_001369347.1:c.3524G>T	R [CGG] > L [CTG]	Coding Sequence Variant
putative Polycomb group protein ASXL2 isoform 3	NP_001356276.1:p.Arg1175L… NP_001356276.1:p.Arg1175Leu	R (Arg) > L (Leu)	Missense Variant
ASXL2 transcript variant 3	NM_001369347.1:c.3524G>C	R [CGG] > P [CCG]	Coding Sequence Variant
putative Polycomb group protein ASXL2 isoform 3	NP_001356276.1:p.Arg1175P… NP_001356276.1:p.Arg1175Pro	R (Arg) > P (Pro)	Missense Variant
ASXL2 transcript variant 3	NM_001369347.1:c.3524G>A	R [CGG] > Q [CAG]	Coding Sequence Variant
putative Polycomb group protein ASXL2 isoform 3	NP_001356276.1:p.Arg1175G… NP_001356276.1:p.Arg1175Gln	R (Arg) > Q (Gln)	Missense Variant
ASXL2 transcript variant 2	NM_001369346.1:c.4130G>T	R [CGG] > L [CTG]	Coding Sequence Variant
putative Polycomb group protein ASXL2 isoform 2	NP_001356275.1:p.Arg1377L… NP_001356275.1:p.Arg1377Leu	R (Arg) > L (Leu)	Missense Variant
ASXL2 transcript variant 2	NM_001369346.1:c.4130G>C	R [CGG] > P [CCG]	Coding Sequence Variant
putative Polycomb group protein ASXL2 isoform 2	NP_001356275.1:p.Arg1377P… NP_001356275.1:p.Arg1377Pro	R (Arg) > P (Pro)	Missense Variant
ASXL2 transcript variant 2	NM_001369346.1:c.4130G>A	R [CGG] > Q [CAG]	Coding Sequence Variant
putative Polycomb group protein ASXL2 isoform 2	NP_001356275.1:p.Arg1377G… NP_001356275.1:p.Arg1377Gln	R (Arg) > Q (Gln)	Missense 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	C=	A	G	T
GRCh38.p14 chr 2	NC_000002.12:g.25742033=	NC_000002.12:g.25742033C>A	NC_000002.12:g.25742033C>G	NC_000002.12:g.25742033C>T
GRCh37.p13 chr 2	NC_000002.11:g.25964902=	NC_000002.11:g.25964902C>A	NC_000002.11:g.25964902C>G	NC_000002.11:g.25964902C>T
ASXL2 RefSeqGene (LRG_1421)	NG_052995.1:g.141484=	NG_052995.1:g.141484G>T	NG_052995.1:g.141484G>C	NG_052995.1:g.141484G>A
ASXL2 transcript variant 1	NM_018263.6:c.4304=	NM_018263.6:c.4304G>T	NM_018263.6:c.4304G>C	NM_018263.6:c.4304G>A
ASXL2 transcript	NM_018263.5:c.4304=	NM_018263.5:c.4304G>T	NM_018263.5:c.4304G>C	NM_018263.5:c.4304G>A
ASXL2 transcript	NM_018263.4:c.4304=	NM_018263.4:c.4304G>T	NM_018263.4:c.4304G>C	NM_018263.4:c.4304G>A
ASXL2 transcript variant 2	NM_001369346.1:c.4130=	NM_001369346.1:c.4130G>T	NM_001369346.1:c.4130G>C	NM_001369346.1:c.4130G>A
ASXL2 transcript variant 3	NM_001369347.1:c.3524=	NM_001369347.1:c.3524G>T	NM_001369347.1:c.3524G>C	NM_001369347.1:c.3524G>A
putative Polycomb group protein ASXL2 isoform 1	NP_060733.4:p.Arg1435=	NP_060733.4:p.Arg1435Leu	NP_060733.4:p.Arg1435Pro	NP_060733.4:p.Arg1435Gln
putative Polycomb group protein ASXL2 isoform 2	NP_001356275.1:p.Arg1377=	NP_001356275.1:p.Arg1377Leu	NP_001356275.1:p.Arg1377Pro	NP_001356275.1:p.Arg1377Gln
putative Polycomb group protein ASXL2 isoform 3	NP_001356276.1:p.Arg1175=	NP_001356276.1:p.Arg1175Leu	NP_001356276.1:p.Arg1175Pro	NP_001356276.1:p.Arg1175Gln

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#.

13 SubSNP, 9 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	1000GENOMES	ss1296350105	Aug 21, 2014 (142)
2	EVA_EXAC	ss1686213340	Apr 01, 2015 (144)
3	ILLUMINA	ss1958398368	Feb 12, 2016 (147)
4	ILLUMINA	ss3021950729	Nov 08, 2017 (151)
5	ILLUMINA	ss3652380033	Oct 11, 2018 (152)
6	ILLUMINA	ss3725766363	Jul 12, 2019 (153)
7	PAGE_CC	ss3770903681	Jul 12, 2019 (153)
8	GNOMAD	ss4037427526	Apr 27, 2021 (155)
9	TOPMED	ss4497966532	Apr 27, 2021 (155)
10	TOPMED	ss4497966533	Apr 27, 2021 (155)
11	EVA	ss5327518628	Oct 17, 2022 (156)
12	1000G_HIGH_COVERAGE	ss5522117849	Oct 17, 2022 (156)
13	EVA	ss5929472617	Oct 17, 2022 (156)
14	1000Genomes	NC_000002.11 - 25964902	Oct 11, 2018 (152)
15	1000Genomes_30x	NC_000002.12 - 25742033	Oct 17, 2022 (156)
16	ExAC	NC_000002.11 - 25964902	Oct 11, 2018 (152)
17	gnomAD - Genomes	NC_000002.12 - 25742033	Apr 27, 2021 (155)
18	gnomAD - Exomes	NC_000002.11 - 25964902	Jul 12, 2019 (153)
19	The PAGE Study	NC_000002.12 - 25742033	Jul 12, 2019 (153)
20	TopMed Submission ignored due to conflicting rows: Row 301789411 (NC_000002.12:25742032:C:G 1/264690) Row 301789412 (NC_000002.12:25742032:C:T 3/264690)	-	Apr 27, 2021 (155)
21	TopMed Submission ignored due to conflicting rows: Row 301789411 (NC_000002.12:25742032:C:G 1/264690) Row 301789412 (NC_000002.12:25742032:C:T 3/264690)	-	Apr 27, 2021 (155)
22	ALFA	NC_000002.12 - 25742033	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
7266722, 6076328, ss1296350105, ss1686213340, ss5327518628	NC_000002.11:25964901:C:A	NC_000002.12:25742032:C:A	(self)
9643784, ss5522117849, ss5929472617	NC_000002.12:25742032:C:A	NC_000002.12:25742032:C:A
5707830717, ss4497966532	NC_000002.12:25742032:C:G	NC_000002.12:25742032:C:G	(self)
1561448, ss1958398368, ss3021950729, ss3652380033	NC_000002.11:25964901:C:T	NC_000002.12:25742032:C:T	(self)
51626664, 125150, 5707830717, ss3725766363, ss3770903681, ss4037427526, ss4497966533	NC_000002.12:25742032:C:T	NC_000002.12:25742032:C:T	(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 rs542810776

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs542810776