Name: rs1491514104
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.

rs1491514104

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr3:15037240-15037244 (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: del(T)₄ / delTT / dupTT
Variation Type: Indel Insertion and Deletion
Frequency: del(T)₄=0.00000 (0/11862, ALFA)
delTT=0.00000 (0/11862, ALFA)
dupTT=0.00000 (0/11862, ALFA)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: NR2C2 : 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	11862	TTTTT=1.00000	T=0.00000, TTT=0.00000, TTTTTTT=0.00000	1.0	N/A
European	Sub	7618	TTTTT=1.0000	T=0.0000, TTT=0.0000, TTTTTTT=0.0000	1.0	N/A
African	Sub	2816	TTTTT=1.0000	T=0.0000, TTT=0.0000, TTTTTTT=0.0000	1.0	N/A
African Others	Sub	108	TTTTT=1.000	T=0.000, TTT=0.000, TTTTTTT=0.000	1.0	N/A
African American	Sub	2708	TTTTT=1.0000	T=0.0000, TTT=0.0000, TTTTTTT=0.0000	1.0	N/A
Asian	Sub	108	TTTTT=1.000	T=0.000, TTT=0.000, TTTTTTT=0.000	1.0	N/A
East Asian	Sub	84	TTTTT=1.00	T=0.00, TTT=0.00, TTTTTTT=0.00	1.0	N/A
Other Asian	Sub	24	TTTTT=1.00	T=0.00, TTT=0.00, TTTTTTT=0.00	1.0	N/A
Latin American 1	Sub	146	TTTTT=1.000	T=0.000, TTT=0.000, TTTTTTT=0.000	1.0	N/A
Latin American 2	Sub	610	TTTTT=1.000	T=0.000, TTT=0.000, TTTTTTT=0.000	1.0	N/A
South Asian	Sub	94	TTTTT=1.00	T=0.00, TTT=0.00, TTTTTTT=0.00	1.0	N/A
Other	Sub	470	TTTTT=1.000	T=0.000, TTT=0.000, TTTTTTT=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").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
Allele Frequency Aggregator	Total	Global	11862	(T)₅=1.00000	del(T)₄=0.00000, delTT=0.00000, dupTT=0.00000
Allele Frequency Aggregator	European	Sub	7618	(T)₅=1.0000	del(T)₄=0.0000, delTT=0.0000, dupTT=0.0000
Allele Frequency Aggregator	African	Sub	2816	(T)₅=1.0000	del(T)₄=0.0000, delTT=0.0000, dupTT=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	610	(T)₅=1.000	del(T)₄=0.000, delTT=0.000, dupTT=0.000
Allele Frequency Aggregator	Other	Sub	470	(T)₅=1.000	del(T)₄=0.000, delTT=0.000, dupTT=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	(T)₅=1.000	del(T)₄=0.000, delTT=0.000, dupTT=0.000
Allele Frequency Aggregator	Asian	Sub	108	(T)₅=1.000	del(T)₄=0.000, delTT=0.000, dupTT=0.000
Allele Frequency Aggregator	South Asian	Sub	94	(T)₅=1.00	del(T)₄=0.00, delTT=0.00, dupTT=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 3	NC_000003.12:g.15037241_15037244del
GRCh38.p14 chr 3	NC_000003.12:g.15037243_15037244del
GRCh38.p14 chr 3	NC_000003.12:g.15037243_15037244dup
GRCh37.p13 chr 3	NC_000003.11:g.15078748_15078751del
GRCh37.p13 chr 3	NC_000003.11:g.15078750_15078751del
GRCh37.p13 chr 3	NC_000003.11:g.15078750_15078751dup

Gene: NR2C2, nuclear receptor subfamily 2 group C member 2 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
NR2C2 transcript variant 2	NM_001291694.2:c.1373-759… NM_001291694.2:c.1373-759_1373-756del	N/A	Intron Variant
NR2C2 transcript variant 1	NM_003298.5:c.1430-759_14… NM_003298.5:c.1430-759_1430-756del	N/A	Intron Variant
NR2C2 transcript variant X1	XM_011534058.4:c.1529-759… XM_011534058.4:c.1529-759_1529-756del	N/A	Intron Variant
NR2C2 transcript variant X5	XM_011534059.3:c.1529-759… XM_011534059.3:c.1529-759_1529-756del	N/A	Intron Variant
NR2C2 transcript variant X3	XM_011534061.4:c.1529-759… XM_011534061.4:c.1529-759_1529-756del	N/A	Intron Variant
NR2C2 transcript variant X10	XM_011534063.4:c.1472-759… XM_011534063.4:c.1472-759_1472-756del	N/A	Intron Variant
NR2C2 transcript variant X15	XM_011534064.4:c.1430-759… XM_011534064.4:c.1430-759_1430-756del	N/A	Intron Variant
NR2C2 transcript variant X16	XM_011534065.4:c.1430-759… XM_011534065.4:c.1430-759_1430-756del	N/A	Intron Variant
NR2C2 transcript variant X17	XM_011534066.4:c.1430-759… XM_011534066.4:c.1430-759_1430-756del	N/A	Intron Variant
NR2C2 transcript variant X23	XM_024453739.2:c.836-759_… XM_024453739.2:c.836-759_836-756del	N/A	Intron Variant
NR2C2 transcript variant X2	XM_047448824.1:c.1529-759… XM_047448824.1:c.1529-759_1529-756del	N/A	Intron Variant
NR2C2 transcript variant X4	XM_047448825.1:c.1529-759… XM_047448825.1:c.1529-759_1529-756del	N/A	Intron Variant
NR2C2 transcript variant X6	XM_047448826.1:c.1529-759… XM_047448826.1:c.1529-759_1529-756del	N/A	Intron Variant
NR2C2 transcript variant X7	XM_047448827.1:c.1529-759… XM_047448827.1:c.1529-759_1529-756del	N/A	Intron Variant
NR2C2 transcript variant X8	XM_047448828.1:c.1529-759… XM_047448828.1:c.1529-759_1529-756del	N/A	Intron Variant
NR2C2 transcript variant X9	XM_047448829.1:c.1529-759… XM_047448829.1:c.1529-759_1529-756del	N/A	Intron Variant
NR2C2 transcript variant X11	XM_047448830.1:c.1472-759… XM_047448830.1:c.1472-759_1472-756del	N/A	Intron Variant
NR2C2 transcript variant X12	XM_047448831.1:c.1472-759… XM_047448831.1:c.1472-759_1472-756del	N/A	Intron Variant
NR2C2 transcript variant X13	XM_047448832.1:c.1472-759… XM_047448832.1:c.1472-759_1472-756del	N/A	Intron Variant
NR2C2 transcript variant X14	XM_047448833.1:c.1472-759… XM_047448833.1:c.1472-759_1472-756del	N/A	Intron Variant
NR2C2 transcript variant X18	XM_047448834.1:c.1430-759… XM_047448834.1:c.1430-759_1430-756del	N/A	Intron Variant
NR2C2 transcript variant X19	XM_047448835.1:c.1373-759… XM_047448835.1:c.1373-759_1373-756del	N/A	Intron Variant
NR2C2 transcript variant X20	XM_047448836.1:c.1472-759… XM_047448836.1:c.1472-759_1472-756del	N/A	Intron Variant
NR2C2 transcript variant X21	XM_047448837.1:c.1472-759… XM_047448837.1:c.1472-759_1472-756del	N/A	Intron Variant
NR2C2 transcript variant X22	XM_047448838.1:c.1430-759… XM_047448838.1:c.1430-759_1430-756del	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	(T)₅=	del(T)₄	delTT	dupTT
GRCh38.p14 chr 3	NC_000003.12:g.15037240_15037244=	NC_000003.12:g.15037241_15037244del	NC_000003.12:g.15037243_15037244del	NC_000003.12:g.15037243_15037244dup
GRCh37.p13 chr 3	NC_000003.11:g.15078747_15078751=	NC_000003.11:g.15078748_15078751del	NC_000003.11:g.15078750_15078751del	NC_000003.11:g.15078750_15078751dup
NR2C2 transcript variant 2	NM_001291694.2:c.1373-760=	NM_001291694.2:c.1373-759_1373-756del	NM_001291694.2:c.1373-757_1373-756del	NM_001291694.2:c.1373-757_1373-756dup
NR2C2 transcript	NM_003298.3:c.1430-760=	NM_003298.3:c.1430-759_1430-756del	NM_003298.3:c.1430-757_1430-756del	NM_003298.3:c.1430-757_1430-756dup
NR2C2 transcript variant 1	NM_003298.5:c.1430-760=	NM_003298.5:c.1430-759_1430-756del	NM_003298.5:c.1430-757_1430-756del	NM_003298.5:c.1430-757_1430-756dup
NR2C2 transcript variant X1	XM_005265428.1:c.1373-760=	XM_005265428.1:c.1373-759_1373-756del	XM_005265428.1:c.1373-757_1373-756del	XM_005265428.1:c.1373-757_1373-756dup
NR2C2 transcript variant X1	XM_011534058.4:c.1529-760=	XM_011534058.4:c.1529-759_1529-756del	XM_011534058.4:c.1529-757_1529-756del	XM_011534058.4:c.1529-757_1529-756dup
NR2C2 transcript variant X5	XM_011534059.3:c.1529-760=	XM_011534059.3:c.1529-759_1529-756del	XM_011534059.3:c.1529-757_1529-756del	XM_011534059.3:c.1529-757_1529-756dup
NR2C2 transcript variant X3	XM_011534061.4:c.1529-760=	XM_011534061.4:c.1529-759_1529-756del	XM_011534061.4:c.1529-757_1529-756del	XM_011534061.4:c.1529-757_1529-756dup
NR2C2 transcript variant X10	XM_011534063.4:c.1472-760=	XM_011534063.4:c.1472-759_1472-756del	XM_011534063.4:c.1472-757_1472-756del	XM_011534063.4:c.1472-757_1472-756dup
NR2C2 transcript variant X15	XM_011534064.4:c.1430-760=	XM_011534064.4:c.1430-759_1430-756del	XM_011534064.4:c.1430-757_1430-756del	XM_011534064.4:c.1430-757_1430-756dup
NR2C2 transcript variant X16	XM_011534065.4:c.1430-760=	XM_011534065.4:c.1430-759_1430-756del	XM_011534065.4:c.1430-757_1430-756del	XM_011534065.4:c.1430-757_1430-756dup
NR2C2 transcript variant X17	XM_011534066.4:c.1430-760=	XM_011534066.4:c.1430-759_1430-756del	XM_011534066.4:c.1430-757_1430-756del	XM_011534066.4:c.1430-757_1430-756dup
NR2C2 transcript variant X23	XM_024453739.2:c.836-760=	XM_024453739.2:c.836-759_836-756del	XM_024453739.2:c.836-757_836-756del	XM_024453739.2:c.836-757_836-756dup
NR2C2 transcript variant X2	XM_047448824.1:c.1529-760=	XM_047448824.1:c.1529-759_1529-756del	XM_047448824.1:c.1529-757_1529-756del	XM_047448824.1:c.1529-757_1529-756dup
NR2C2 transcript variant X4	XM_047448825.1:c.1529-760=	XM_047448825.1:c.1529-759_1529-756del	XM_047448825.1:c.1529-757_1529-756del	XM_047448825.1:c.1529-757_1529-756dup
NR2C2 transcript variant X6	XM_047448826.1:c.1529-760=	XM_047448826.1:c.1529-759_1529-756del	XM_047448826.1:c.1529-757_1529-756del	XM_047448826.1:c.1529-757_1529-756dup
NR2C2 transcript variant X7	XM_047448827.1:c.1529-760=	XM_047448827.1:c.1529-759_1529-756del	XM_047448827.1:c.1529-757_1529-756del	XM_047448827.1:c.1529-757_1529-756dup
NR2C2 transcript variant X8	XM_047448828.1:c.1529-760=	XM_047448828.1:c.1529-759_1529-756del	XM_047448828.1:c.1529-757_1529-756del	XM_047448828.1:c.1529-757_1529-756dup
NR2C2 transcript variant X9	XM_047448829.1:c.1529-760=	XM_047448829.1:c.1529-759_1529-756del	XM_047448829.1:c.1529-757_1529-756del	XM_047448829.1:c.1529-757_1529-756dup
NR2C2 transcript variant X11	XM_047448830.1:c.1472-760=	XM_047448830.1:c.1472-759_1472-756del	XM_047448830.1:c.1472-757_1472-756del	XM_047448830.1:c.1472-757_1472-756dup
NR2C2 transcript variant X12	XM_047448831.1:c.1472-760=	XM_047448831.1:c.1472-759_1472-756del	XM_047448831.1:c.1472-757_1472-756del	XM_047448831.1:c.1472-757_1472-756dup
NR2C2 transcript variant X13	XM_047448832.1:c.1472-760=	XM_047448832.1:c.1472-759_1472-756del	XM_047448832.1:c.1472-757_1472-756del	XM_047448832.1:c.1472-757_1472-756dup
NR2C2 transcript variant X14	XM_047448833.1:c.1472-760=	XM_047448833.1:c.1472-759_1472-756del	XM_047448833.1:c.1472-757_1472-756del	XM_047448833.1:c.1472-757_1472-756dup
NR2C2 transcript variant X18	XM_047448834.1:c.1430-760=	XM_047448834.1:c.1430-759_1430-756del	XM_047448834.1:c.1430-757_1430-756del	XM_047448834.1:c.1430-757_1430-756dup
NR2C2 transcript variant X19	XM_047448835.1:c.1373-760=	XM_047448835.1:c.1373-759_1373-756del	XM_047448835.1:c.1373-757_1373-756del	XM_047448835.1:c.1373-757_1373-756dup
NR2C2 transcript variant X20	XM_047448836.1:c.1472-760=	XM_047448836.1:c.1472-759_1472-756del	XM_047448836.1:c.1472-757_1472-756del	XM_047448836.1:c.1472-757_1472-756dup
NR2C2 transcript variant X21	XM_047448837.1:c.1472-760=	XM_047448837.1:c.1472-759_1472-756del	XM_047448837.1:c.1472-757_1472-756del	XM_047448837.1:c.1472-757_1472-756dup
NR2C2 transcript variant X22	XM_047448838.1:c.1430-760=	XM_047448838.1:c.1430-759_1430-756del	XM_047448838.1:c.1430-757_1430-756del	XM_047448838.1:c.1430-757_1430-756dup

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	GNOMAD	ss4066314980	Apr 26, 2021 (155)
2	GNOMAD	ss4066314982	Apr 26, 2021 (155)
3	GNOMAD	ss4066314983	Apr 26, 2021 (155)
4	TOPMED	ss4555149436	Apr 26, 2021 (155)
5	TOPMED	ss4555149438	Apr 26, 2021 (155)
6	HUGCELL_USP	ss5452636822	Oct 13, 2022 (156)
7	gnomAD - Genomes Submission ignored due to conflicting rows: Row 99825327 (NC_000003.12:15037239::TT 6/137562) Row 99825329 (NC_000003.12:15037239:TT: 3/137562) Row 99825330 (NC_000003.12:15037239:TTTT: 1/137564)	-	Apr 26, 2021 (155)
8	gnomAD - Genomes Submission ignored due to conflicting rows: Row 99825327 (NC_000003.12:15037239::TT 6/137562) Row 99825329 (NC_000003.12:15037239:TT: 3/137562) Row 99825330 (NC_000003.12:15037239:TTTT: 1/137564)	-	Apr 26, 2021 (155)
9	gnomAD - Genomes Submission ignored due to conflicting rows: Row 99825327 (NC_000003.12:15037239::TT 6/137562) Row 99825329 (NC_000003.12:15037239:TT: 3/137562) Row 99825330 (NC_000003.12:15037239:TTTT: 1/137564)	-	Apr 26, 2021 (155)
10	TopMed Submission ignored due to conflicting rows: Row 392526991 (NC_000003.12:15037239::TT 1/264690) Row 392526993 (NC_000003.12:15037239:TTTT: 1/264690)	-	Apr 26, 2021 (155)
11	TopMed Submission ignored due to conflicting rows: Row 392526991 (NC_000003.12:15037239::TT 1/264690) Row 392526993 (NC_000003.12:15037239:TTTT: 1/264690)	-	Apr 26, 2021 (155)
12	ALFA	NC_000003.12 - 15037240	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
ss4066314983, ss4555149438	NC_000003.12:15037239:TTTT:	NC_000003.12:15037239:TTTTT:T	(self)
342408264	NC_000003.12:15037239:TTTTT:T	NC_000003.12:15037239:TTTTT:T	(self)
ss4066314982, ss5452636822	NC_000003.12:15037239:TT:	NC_000003.12:15037239:TTTTT:TTT	(self)
342408264	NC_000003.12:15037239:TTTTT:TTT	NC_000003.12:15037239:TTTTT:TTT	(self)
ss4066314980, ss4555149436	NC_000003.12:15037239::TT	NC_000003.12:15037239:TTTTT:TTTTTTT	(self)
342408264	NC_000003.12:15037239:TTTTT:TTTTTTT	NC_000003.12:15037239:TTTTT:TTTTTTT	(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 rs1491514104

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

rs1491514104