Name: rs1043863652
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.

rs1043863652

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr10:18646547-18646556 (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: delA / dupA
Variation Type: Indel Insertion and Deletion
Frequency: delA=0.00000 (0/14048, ALFA)
dupA=0.00000 (0/14048, ALFA)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: NSUN6 : Intron 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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	HWEP
Total	Global	14048	AAAAAAAAAA=1.00000	AAAAAAAAA=0.00000, AAAAAAAAAAA=0.00000	1.0	N/A
European	Sub	9688	AAAAAAAAAA=1.0000	AAAAAAAAA=0.0000, AAAAAAAAAAA=0.0000	1.0	N/A
African	Sub	2898	AAAAAAAAAA=1.0000	AAAAAAAAA=0.0000, AAAAAAAAAAA=0.0000	1.0	N/A
African Others	Sub	114	AAAAAAAAAA=1.000	AAAAAAAAA=0.000, AAAAAAAAAAA=0.000	1.0	N/A
African American	Sub	2784	AAAAAAAAAA=1.0000	AAAAAAAAA=0.0000, AAAAAAAAAAA=0.0000	1.0	N/A
Asian	Sub	112	AAAAAAAAAA=1.000	AAAAAAAAA=0.000, AAAAAAAAAAA=0.000	1.0	N/A
East Asian	Sub	86	AAAAAAAAAA=1.00	AAAAAAAAA=0.00, AAAAAAAAAAA=0.00	1.0	N/A
Other Asian	Sub	26	AAAAAAAAAA=1.00	AAAAAAAAA=0.00, AAAAAAAAAAA=0.00	1.0	N/A
Latin American 1	Sub	146	AAAAAAAAAA=1.000	AAAAAAAAA=0.000, AAAAAAAAAAA=0.000	1.0	N/A
Latin American 2	Sub	610	AAAAAAAAAA=1.000	AAAAAAAAA=0.000, AAAAAAAAAAA=0.000	1.0	N/A
South Asian	Sub	98	AAAAAAAAAA=1.00	AAAAAAAAA=0.00, AAAAAAAAAAA=0.00	1.0	N/A
Other	Sub	496	AAAAAAAAAA=1.000	AAAAAAAAA=0.000, AAAAAAAAAAA=0.000	1.0	N/A

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
Allele Frequency Aggregator	Total	Global	14048	(A)₁₀=1.00000	delA=0.00000, dupA=0.00000
Allele Frequency Aggregator	European	Sub	9688	(A)₁₀=1.0000	delA=0.0000, dupA=0.0000
Allele Frequency Aggregator	African	Sub	2898	(A)₁₀=1.0000	delA=0.0000, dupA=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	610	(A)₁₀=1.000	delA=0.000, dupA=0.000
Allele Frequency Aggregator	Other	Sub	496	(A)₁₀=1.000	delA=0.000, dupA=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	(A)₁₀=1.000	delA=0.000, dupA=0.000
Allele Frequency Aggregator	Asian	Sub	112	(A)₁₀=1.000	delA=0.000, dupA=0.000
Allele Frequency Aggregator	South Asian	Sub	98	(A)₁₀=1.00	delA=0.00, dupA=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 10	NC_000010.11:g.18646556del
GRCh38.p14 chr 10	NC_000010.11:g.18646556dup
GRCh37.p13 chr 10	NC_000010.10:g.18935485del
GRCh37.p13 chr 10	NC_000010.10:g.18935485dup

Gene: NSUN6, NOP2/Sun RNA methyltransferase 6 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
NSUN6 transcript variant 2	NM_001351115.2:c.231+1943… NM_001351115.2:c.231+1943del	N/A	Intron Variant
NSUN6 transcript variant 3	NM_001351116.2:c.195+1943… NM_001351116.2:c.195+1943del	N/A	Intron Variant
NSUN6 transcript variant 4	NM_001351117.2:c.76-3992d… NM_001351117.2:c.76-3992del	N/A	Intron Variant
NSUN6 transcript variant 5	NM_001351118.2:c.-113+458… NM_001351118.2:c.-113+4582del	N/A	Intron Variant
NSUN6 transcript variant 1	NM_182543.5:c.231+1943del	N/A	Intron Variant
NSUN6 transcript variant X2	XM_011519383.2:c.231+1943… XM_011519383.2:c.231+1943del	N/A	Intron Variant
NSUN6 transcript variant X5	XM_011519384.2:c.195+1943… XM_011519384.2:c.195+1943del	N/A	Intron Variant
NSUN6 transcript variant X3	XM_011519385.2:c.195+1943… XM_011519385.2:c.195+1943del	N/A	Intron Variant
NSUN6 transcript variant X6	XM_011519386.3:c.195+1943… XM_011519386.3:c.195+1943del	N/A	Intron Variant
NSUN6 transcript variant X10	XM_011519387.3:c.76-3992d… XM_011519387.3:c.76-3992del	N/A	Intron Variant
NSUN6 transcript variant X4	XM_017015907.3:c.195+1943… XM_017015907.3:c.195+1943del	N/A	Intron Variant
NSUN6 transcript variant X7	XM_024447884.2:c.195+1943… XM_024447884.2:c.195+1943del	N/A	Intron Variant
NSUN6 transcript variant X1	XM_047424777.1:c.231+1943… XM_047424777.1:c.231+1943del	N/A	Intron Variant
NSUN6 transcript variant X8	XM_047424778.1:c.195+1943… XM_047424778.1:c.195+1943del	N/A	Intron Variant
NSUN6 transcript variant X9	XM_047424779.1:c.195+1943… XM_047424779.1:c.195+1943del	N/A	Intron Variant
NSUN6 transcript variant X11	XM_047424780.1:c.231+1943… XM_047424780.1:c.231+1943del	N/A	Intron Variant
NSUN6 transcript variant X12	XM_047424781.1:c.14+1943d… XM_047424781.1:c.14+1943del	N/A	Intron Variant
NSUN6 transcript variant X13	XM_047424782.1:c.231+1943… XM_047424782.1:c.231+1943del	N/A	Intron Variant
NSUN6 transcript variant X16	XM_047424784.1:c.231+1943… XM_047424784.1:c.231+1943del	N/A	Intron Variant
NSUN6 transcript variant X15	XM_017015912.3:c.	N/A	Genic Upstream Transcript Variant
NSUN6 transcript variant X14	XM_047424783.1:c.	N/A	Genic Upstream 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	(A)₁₀=	delA	dupA
GRCh38.p14 chr 10	NC_000010.11:g.18646547_18646556=	NC_000010.11:g.18646556del	NC_000010.11:g.18646556dup
GRCh37.p13 chr 10	NC_000010.10:g.18935476_18935485=	NC_000010.10:g.18935485del	NC_000010.10:g.18935485dup
NSUN6 transcript variant 2	NM_001351115.2:c.231+1943=	NM_001351115.2:c.231+1943del	NM_001351115.2:c.231+1943dup
NSUN6 transcript variant 3	NM_001351116.2:c.195+1943=	NM_001351116.2:c.195+1943del	NM_001351116.2:c.195+1943dup
NSUN6 transcript variant 4	NM_001351117.2:c.76-3992=	NM_001351117.2:c.76-3992del	NM_001351117.2:c.76-3992dup
NSUN6 transcript variant 5	NM_001351118.2:c.-113+4582=	NM_001351118.2:c.-113+4582del	NM_001351118.2:c.-113+4582dup
NSUN6 transcript	NM_182543.2:c.231+1943=	NM_182543.2:c.231+1943del	NM_182543.2:c.231+1943dup
NSUN6 transcript variant 1	NM_182543.5:c.231+1943=	NM_182543.5:c.231+1943del	NM_182543.5:c.231+1943dup
NSUN6 transcript variant X1	XM_005252394.1:c.231+1943=	XM_005252394.1:c.231+1943del	XM_005252394.1:c.231+1943dup
NSUN6 transcript variant X2	XM_005252395.1:c.195+1943=	XM_005252395.1:c.195+1943del	XM_005252395.1:c.195+1943dup
NSUN6 transcript variant X3	XM_005252396.1:c.195+1943=	XM_005252396.1:c.195+1943del	XM_005252396.1:c.195+1943dup
NSUN6 transcript variant X4	XM_005252397.1:c.76-3992=	XM_005252397.1:c.76-3992del	XM_005252397.1:c.76-3992dup
NSUN6 transcript variant X5	XM_005252398.1:c.14+1943=	XM_005252398.1:c.14+1943del	XM_005252398.1:c.14+1943dup
NSUN6 transcript variant X6	XM_005252399.1:c.-113+4582=	XM_005252399.1:c.-113+4582del	XM_005252399.1:c.-113+4582dup
NSUN6 transcript variant X2	XM_011519383.2:c.231+1943=	XM_011519383.2:c.231+1943del	XM_011519383.2:c.231+1943dup
NSUN6 transcript variant X5	XM_011519384.2:c.195+1943=	XM_011519384.2:c.195+1943del	XM_011519384.2:c.195+1943dup
NSUN6 transcript variant X3	XM_011519385.2:c.195+1943=	XM_011519385.2:c.195+1943del	XM_011519385.2:c.195+1943dup
NSUN6 transcript variant X6	XM_011519386.3:c.195+1943=	XM_011519386.3:c.195+1943del	XM_011519386.3:c.195+1943dup
NSUN6 transcript variant X10	XM_011519387.3:c.76-3992=	XM_011519387.3:c.76-3992del	XM_011519387.3:c.76-3992dup
NSUN6 transcript variant X4	XM_017015907.3:c.195+1943=	XM_017015907.3:c.195+1943del	XM_017015907.3:c.195+1943dup
NSUN6 transcript variant X7	XM_024447884.2:c.195+1943=	XM_024447884.2:c.195+1943del	XM_024447884.2:c.195+1943dup
NSUN6 transcript variant X1	XM_047424777.1:c.231+1943=	XM_047424777.1:c.231+1943del	XM_047424777.1:c.231+1943dup
NSUN6 transcript variant X8	XM_047424778.1:c.195+1943=	XM_047424778.1:c.195+1943del	XM_047424778.1:c.195+1943dup
NSUN6 transcript variant X9	XM_047424779.1:c.195+1943=	XM_047424779.1:c.195+1943del	XM_047424779.1:c.195+1943dup
NSUN6 transcript variant X11	XM_047424780.1:c.231+1943=	XM_047424780.1:c.231+1943del	XM_047424780.1:c.231+1943dup
NSUN6 transcript variant X12	XM_047424781.1:c.14+1943=	XM_047424781.1:c.14+1943del	XM_047424781.1:c.14+1943dup
NSUN6 transcript variant X13	XM_047424782.1:c.231+1943=	XM_047424782.1:c.231+1943del	XM_047424782.1:c.231+1943dup
NSUN6 transcript variant X16	XM_047424784.1:c.231+1943=	XM_047424784.1:c.231+1943del	XM_047424784.1:c.231+1943dup

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	GNOMAD	ss4214000206	Apr 26, 2021 (155)
2	GNOMAD	ss4214000207	Apr 26, 2021 (155)
3	TOPMED	ss4844514836	Apr 26, 2021 (155)
4	TOPMED	ss4844514837	Apr 26, 2021 (155)
5	gnomAD - Genomes Submission ignored due to conflicting rows: Row 345205880 (NC_000010.11:18646546::A 2/32310) Row 345205881 (NC_000010.11:18646546:A: 6/32308)	-	Apr 26, 2021 (155)
6	gnomAD - Genomes Submission ignored due to conflicting rows: Row 345205880 (NC_000010.11:18646546::A 2/32310) Row 345205881 (NC_000010.11:18646546:A: 6/32308)	-	Apr 26, 2021 (155)
7	TopMed Submission ignored due to conflicting rows: Row 60060491 (NC_000010.11:18646546::A 10/264690) Row 60060492 (NC_000010.11:18646546:A: 10/264690)	-	Apr 26, 2021 (155)
8	TopMed Submission ignored due to conflicting rows: Row 60060491 (NC_000010.11:18646546::A 10/264690) Row 60060492 (NC_000010.11:18646546:A: 10/264690)	-	Apr 26, 2021 (155)
9	ALFA	NC_000010.11 - 18646547	Apr 26, 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
ss4214000207, ss4844514837	NC_000010.11:18646546:A:	NC_000010.11:18646546:AAAAAAAAAA:A… NC_000010.11:18646546:AAAAAAAAAA:AAAAAAAAA	(self)
3865067014	NC_000010.11:18646546:AAAAAAAAAA:A… NC_000010.11:18646546:AAAAAAAAAA:AAAAAAAAA	NC_000010.11:18646546:AAAAAAAAAA:A… NC_000010.11:18646546:AAAAAAAAAA:AAAAAAAAA	(self)
ss4214000206, ss4844514836	NC_000010.11:18646546::A	NC_000010.11:18646546:AAAAAAAAAA:A… NC_000010.11:18646546:AAAAAAAAAA:AAAAAAAAAAA	(self)
3865067014	NC_000010.11:18646546:AAAAAAAAAA:A… NC_000010.11:18646546:AAAAAAAAAA:AAAAAAAAAAA	NC_000010.11:18646546:AAAAAAAAAA:A… NC_000010.11:18646546:AAAAAAAAAA:AAAAAAAAAAA	(self)

Removed from this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Destination RSIDs
ss2335882558	NC_000010.10:18935475:A:	NC_000010.11:18646546:AAAAAAAAAA:A… NC_000010.11:18646546:AAAAAAAAAA:AAAAAAAAA

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

No publications for rs1043863652

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

rs1043863652