Name: rs1338274451
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.

rs1338274451

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chrX:66036822-66036831 (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: delTA / dupTA
Variation Type: Indel Insertion and Deletion
Frequency: dupTA=0.00006 (1/17506, 14KJPN)
delTA=0.00007 (1/15148, ALFA)
dupTA=0.00009 (1/11478, 8.3KJPN)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: VSIG4 : 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	HTRZ	HWEP
Total	Global	15148	TATATATATA=0.99993	TATATATA=0.00007, TATATATATATA=0.00000	0.999868	0.000132	0
European	Sub	10900	TATATATATA=0.99991	TATATATA=0.00009, TATATATATATA=0.00000	0.999817	0.000183	0
African	Sub	2814	TATATATATA=1.0000	TATATATA=0.0000, TATATATATATA=0.0000	1.0	0.0	N/A
African Others	Sub	108	TATATATATA=1.000	TATATATA=0.000, TATATATATATA=0.000	1.0	0.0	N/A
African American	Sub	2706	TATATATATA=1.0000	TATATATA=0.0000, TATATATATATA=0.0000	1.0	0.0	N/A
Asian	Sub	108	TATATATATA=1.000	TATATATA=0.000, TATATATATATA=0.000	1.0	0.0	N/A
East Asian	Sub	84	TATATATATA=1.00	TATATATA=0.00, TATATATATATA=0.00	1.0	0.0	N/A
Other Asian	Sub	24	TATATATATA=1.00	TATATATA=0.00, TATATATATATA=0.00	1.0	0.0	N/A
Latin American 1	Sub	146	TATATATATA=1.000	TATATATA=0.000, TATATATATATA=0.000	1.0	0.0	N/A
Latin American 2	Sub	610	TATATATATA=1.000	TATATATA=0.000, TATATATATATA=0.000	1.0	0.0	N/A
South Asian	Sub	94	TATATATATA=1.00	TATATATA=0.00, TATATATATATA=0.00	1.0	0.0	N/A
Other	Sub	476	TATATATATA=1.000	TATATATA=0.000, TATATATATATA=0.000	1.0	0.0	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").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
14KJPN	JAPANESE	Study-wide	17506	- No frequency provided	dupTA=0.00006
Allele Frequency Aggregator	Total	Global	15148	(TA)₅=0.99993	delTA=0.00007, dupTA=0.00000
Allele Frequency Aggregator	European	Sub	10900	(TA)₅=0.99991	delTA=0.00009, dupTA=0.00000
Allele Frequency Aggregator	African	Sub	2814	(TA)₅=1.0000	delTA=0.0000, dupTA=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	610	(TA)₅=1.000	delTA=0.000, dupTA=0.000
Allele Frequency Aggregator	Other	Sub	476	(TA)₅=1.000	delTA=0.000, dupTA=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	(TA)₅=1.000	delTA=0.000, dupTA=0.000
Allele Frequency Aggregator	Asian	Sub	108	(TA)₅=1.000	delTA=0.000, dupTA=0.000
Allele Frequency Aggregator	South Asian	Sub	94	(TA)₅=1.00	delTA=0.00, dupTA=0.00
8.3KJPN	JAPANESE	Study-wide	11478	- No frequency provided	dupTA=0.00009

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 X	NC_000023.11:g.66036822TA[4]
GRCh38.p14 chr X	NC_000023.11:g.66036822TA[6]
GRCh37.p13 chr X	NC_000023.10:g.65256664TA[4]
GRCh37.p13 chr X	NC_000023.10:g.65256664TA[6]
VSIG4 RefSeqGene	NG_021306.1:g.8295TA[4]
VSIG4 RefSeqGene	NG_021306.1:g.8295TA[6]

Gene: VSIG4, V-set and immunoglobulin domain containing 4 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
VSIG4 transcript variant 2	NM_001100431.2:c.56-3001T… NM_001100431.2:c.56-3001TA[4]	N/A	Intron Variant
VSIG4 transcript variant 4	NM_001184830.2:c.56-3001T… NM_001184830.2:c.56-3001TA[4]	N/A	Intron Variant
VSIG4 transcript variant 3	NM_001184831.2:c.56-3001T… NM_001184831.2:c.56-3001TA[4]	N/A	Intron Variant
VSIG4 transcript variant 5	NM_001257403.2:c.56-3001T… NM_001257403.2:c.56-3001TA[4]	N/A	Intron Variant
VSIG4 transcript variant 1	NM_007268.3:c.56-3001TA[4]	N/A	Intron 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	(TA)₅=	delTA	dupTA
GRCh38.p14 chr X	NC_000023.11:g.66036822_66036831=	NC_000023.11:g.66036822TA[4]	NC_000023.11:g.66036822TA[6]
GRCh37.p13 chr X	NC_000023.10:g.65256664_65256673=	NC_000023.10:g.65256664TA[4]	NC_000023.10:g.65256664TA[6]
VSIG4 RefSeqGene	NG_021306.1:g.8295_8304=	NG_021306.1:g.8295TA[4]	NG_021306.1:g.8295TA[6]
VSIG4 transcript variant 2	NM_001100431.1:c.56-2992=	NM_001100431.1:c.56-3001TA[4]	NM_001100431.1:c.56-3001TA[6]
VSIG4 transcript variant 2	NM_001100431.2:c.56-2992=	NM_001100431.2:c.56-3001TA[4]	NM_001100431.2:c.56-3001TA[6]
VSIG4 transcript variant 4	NM_001184830.1:c.56-2992=	NM_001184830.1:c.56-3001TA[4]	NM_001184830.1:c.56-3001TA[6]
VSIG4 transcript variant 4	NM_001184830.2:c.56-2992=	NM_001184830.2:c.56-3001TA[4]	NM_001184830.2:c.56-3001TA[6]
VSIG4 transcript variant 3	NM_001184831.1:c.56-2992=	NM_001184831.1:c.56-3001TA[4]	NM_001184831.1:c.56-3001TA[6]
VSIG4 transcript variant 3	NM_001184831.2:c.56-2992=	NM_001184831.2:c.56-3001TA[4]	NM_001184831.2:c.56-3001TA[6]
VSIG4 transcript variant 5	NM_001257403.1:c.56-2992=	NM_001257403.1:c.56-3001TA[4]	NM_001257403.1:c.56-3001TA[6]
VSIG4 transcript variant 5	NM_001257403.2:c.56-2992=	NM_001257403.2:c.56-3001TA[4]	NM_001257403.2:c.56-3001TA[6]
VSIG4 transcript variant 1	NM_007268.2:c.56-2992=	NM_007268.2:c.56-3001TA[4]	NM_007268.2:c.56-3001TA[6]
VSIG4 transcript variant 1	NM_007268.3:c.56-2992=	NM_007268.3:c.56-3001TA[4]	NM_007268.3:c.56-3001TA[6]
VSIG4 transcript variant X1	XM_005262240.1:c.56-2992=	XM_005262240.1:c.56-3001TA[4]	XM_005262240.1:c.56-3001TA[6]

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	ss4372751883	Apr 27, 2021 (155)
2	GNOMAD	ss4372751884	Apr 27, 2021 (155)
3	TOMMO_GENOMICS	ss5234734051	Apr 27, 2021 (155)
4	TOMMO_GENOMICS	ss5796639689	Oct 17, 2022 (156)
5	gnomAD - Genomes Submission ignored due to conflicting rows: Row 582322095 (NC_000023.11:66036821::TA 2/38939) Row 582322096 (NC_000023.11:66036821:TA: 23/38939)	-	Apr 27, 2021 (155)
6	gnomAD - Genomes Submission ignored due to conflicting rows: Row 582322095 (NC_000023.11:66036821::TA 2/38939) Row 582322096 (NC_000023.11:66036821:TA: 23/38939)	-	Apr 27, 2021 (155)
7	8.3KJPN	NC_000023.10 - 65256664	Apr 27, 2021 (155)
8	14KJPN	NC_000023.11 - 66036822	Oct 17, 2022 (156)
9	ALFA	NC_000023.11 - 66036822	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
ss4372751884	NC_000023.11:66036821:TA:	NC_000023.11:66036821:TATATATATA:T… NC_000023.11:66036821:TATATATATA:TATATATA	(self)
8692716659	NC_000023.11:66036821:TATATATATA:T… NC_000023.11:66036821:TATATATATA:TATATATA	NC_000023.11:66036821:TATATATATA:T… NC_000023.11:66036821:TATATATATA:TATATATA	(self)
92703358, ss5234734051	NC_000023.10:65256663::TA	NC_000023.11:66036821:TATATATATA:T… NC_000023.11:66036821:TATATATATA:TATATATATATA	(self)
130476793, ss4372751883, ss5796639689	NC_000023.11:66036821::TA	NC_000023.11:66036821:TATATATATA:T… NC_000023.11:66036821:TATATATATA:TATATATATATA	(self)
8692716659	NC_000023.11:66036821:TATATATATA:T… NC_000023.11:66036821:TATATATATA:TATATATATATA	NC_000023.11:66036821:TATATATATA:T… NC_000023.11:66036821:TATATATATA:TATATATATATA	(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 rs1338274451

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

rs1338274451