Name: rs1491521915
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.

rs1491521915

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chrX:132396500-132396501 (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: delCT
Variation Type: Deletion
Frequency: delCT=0.00463 (274/59136, GnomAD)
delCT=0.00759 (90/11862, ALFA)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: MBNL3 : Intron Variant
RAP2C-AS1 : 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	Alt HMOZ	HTRZ	HWEP
Total	Global	11862	CT=0.99241	=0.00759	0.988366	0.003541	0.008093	32
European	Sub	7618	CT=0.9999	=0.0001	0.999737	0.0	0.000263	0
African	Sub	2816	CT=0.9695	=0.0305	0.953835	0.014915	0.03125	32
African Others	Sub	108	CT=0.954	=0.046	0.925926	0.018519	0.055556	5
African American	Sub	2708	CT=0.9701	=0.0299	0.954948	0.014771	0.030281	32
Asian	Sub	108	CT=1.000	=0.000	1.0	0.0	0.0	N/A
East Asian	Sub	84	CT=1.00	=0.00	1.0	0.0	0.0	N/A
Other Asian	Sub	24	CT=1.00	=0.00	1.0	0.0	0.0	N/A
Latin American 1	Sub	146	CT=1.000	=0.000	1.0	0.0	0.0	N/A
Latin American 2	Sub	610	CT=0.998	=0.002	0.996721	0.0	0.003279	0
South Asian	Sub	94	CT=1.00	=0.00	1.0	0.0	0.0	N/A
Other	Sub	470	CT=0.996	=0.004	0.991489	0.0	0.008511	0

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
gnomAD - Genomes	Global	Study-wide	59136	CT=0.99537	delCT=0.00463
gnomAD - Genomes	European	Sub	37121	CT=0.99987	delCT=0.00013
gnomAD - Genomes	African	Sub	14114	CT=0.98158	delCT=0.01842
gnomAD - Genomes	American	Sub	3794	CT=0.9979	delCT=0.0021
gnomAD - Genomes	Ashkenazi Jewish	Sub	1840	CT=1.0000	delCT=0.0000
gnomAD - Genomes	East Asian	Sub	1483	CT=1.0000	delCT=0.0000
gnomAD - Genomes	Other	Sub	784	CT=0.999	delCT=0.001
Allele Frequency Aggregator	Total	Global	11862	CT=0.99241	delCT=0.00759
Allele Frequency Aggregator	European	Sub	7618	CT=0.9999	delCT=0.0001
Allele Frequency Aggregator	African	Sub	2816	CT=0.9695	delCT=0.0305
Allele Frequency Aggregator	Latin American 2	Sub	610	CT=0.998	delCT=0.002
Allele Frequency Aggregator	Other	Sub	470	CT=0.996	delCT=0.004
Allele Frequency Aggregator	Latin American 1	Sub	146	CT=1.000	delCT=0.000
Allele Frequency Aggregator	Asian	Sub	108	CT=1.000	delCT=0.000
Allele Frequency Aggregator	South Asian	Sub	94	CT=1.00	delCT=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 X	NC_000023.11:g.132396500_132396501del
GRCh37.p13 chr X	NC_000023.10:g.131530528_131530529del
MBNL3 RefSeqGene	NG_016324.2:g.98468_98469del

Gene: MBNL3, muscleblind like splicing regulator 3 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
MBNL3 transcript variant 3	NM_001170701.3:c.55-4167_… NM_001170701.3:c.55-4167_55-4166del	N/A	Intron Variant
MBNL3 transcript variant 4	NM_001170702.3:c.55-4167_… NM_001170702.3:c.55-4167_55-4166del	N/A	Intron Variant
MBNL3 transcript variant 5	NM_001170703.2:c.55-4167_… NM_001170703.2:c.55-4167_55-4166del	N/A	Intron Variant
MBNL3 transcript variant 6	NM_001170704.2:c.55-4167_… NM_001170704.2:c.55-4167_55-4166del	N/A	Intron Variant
MBNL3 transcript variant 7	NM_001386889.1:c.343-4167… NM_001386889.1:c.343-4167_343-4166del	N/A	Intron Variant
MBNL3 transcript variant 8	NM_001386891.1:c.343-4167… NM_001386891.1:c.343-4167_343-4166del	N/A	Intron Variant
MBNL3 transcript variant 9	NM_001386892.1:c.343-4167… NM_001386892.1:c.343-4167_343-4166del	N/A	Intron Variant
MBNL3 transcript variant 10	NM_001386894.1:c.343-4167… NM_001386894.1:c.343-4167_343-4166del	N/A	Intron Variant
MBNL3 transcript variant 11	NM_001386896.1:c.343-4167… NM_001386896.1:c.343-4167_343-4166del	N/A	Intron Variant
MBNL3 transcript variant 12	NM_001386897.1:c.343-4167… NM_001386897.1:c.343-4167_343-4166del	N/A	Intron Variant
MBNL3 transcript variant 13	NM_001386898.1:c.343-4167… NM_001386898.1:c.343-4167_343-4166del	N/A	Intron Variant
MBNL3 transcript variant 14	NM_001386899.1:c.343-4167… NM_001386899.1:c.343-4167_343-4166del	N/A	Intron Variant
MBNL3 transcript variant 15	NM_001386900.1:c.55-4167_… NM_001386900.1:c.55-4167_55-4166del	N/A	Intron Variant
MBNL3 transcript variant 16	NM_001386901.1:c.55-4167_… NM_001386901.1:c.55-4167_55-4166del	N/A	Intron Variant
MBNL3 transcript variant 17	NM_001386902.1:c.55-4167_… NM_001386902.1:c.55-4167_55-4166del	N/A	Intron Variant
MBNL3 transcript variant 18	NM_001386907.1:c.55-4167_… NM_001386907.1:c.55-4167_55-4166del	N/A	Intron Variant
MBNL3 transcript variant 19	NM_001386909.1:c.55-4167_… NM_001386909.1:c.55-4167_55-4166del	N/A	Intron Variant
MBNL3 transcript variant 20	NM_001386910.1:c.55-4167_… NM_001386910.1:c.55-4167_55-4166del	N/A	Intron Variant
MBNL3 transcript variant 21	NM_001386911.1:c.55-4167_… NM_001386911.1:c.55-4167_55-4166del	N/A	Intron Variant
MBNL3 transcript variant 22	NM_001386912.1:c.55-4167_… NM_001386912.1:c.55-4167_55-4166del	N/A	Intron Variant
MBNL3 transcript variant 23	NM_001386913.1:c.55-4167_… NM_001386913.1:c.55-4167_55-4166del	N/A	Intron Variant
MBNL3 transcript variant 24	NM_001386914.1:c.55-4167_… NM_001386914.1:c.55-4167_55-4166del	N/A	Intron Variant
MBNL3 transcript variant 25	NM_001386915.1:c.55-4167_… NM_001386915.1:c.55-4167_55-4166del	N/A	Intron Variant
MBNL3 transcript variant 26	NM_001386916.1:c.-12-4167… NM_001386916.1:c.-12-4167_-12-4166del	N/A	Intron Variant
MBNL3 transcript variant 27	NM_001386917.1:c.55-4167_… NM_001386917.1:c.55-4167_55-4166del	N/A	Intron Variant
MBNL3 transcript variant 28	NM_001386918.1:c.55-4167_… NM_001386918.1:c.55-4167_55-4166del	N/A	Intron Variant
MBNL3 transcript variant 1	NM_018388.4:c.343-4167_34… NM_018388.4:c.343-4167_343-4166del	N/A	Intron Variant
MBNL3 transcript variant 2	NM_133486.4:c.343-4167_34… NM_133486.4:c.343-4167_343-4166del	N/A	Intron Variant
MBNL3 transcript variant X2	XM_024452403.2:c.217-4167… XM_024452403.2:c.217-4167_217-4166del	N/A	Intron Variant
MBNL3 transcript variant X1	XM_047442250.1:c.178-4167… XM_047442250.1:c.178-4167_178-4166del	N/A	Intron Variant
MBNL3 transcript variant X3	XM_047442251.1:c.169-4167… XM_047442251.1:c.169-4167_169-4166del	N/A	Intron Variant

Gene: RAP2C-AS1, RAP2C antisense RNA 1 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
RAP2C-AS1 transcript	NR_110410.1:n.	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	CT=	delCT
GRCh38.p14 chr X	NC_000023.11:g.132396500_132396501=	NC_000023.11:g.132396500_132396501del
GRCh37.p13 chr X	NC_000023.10:g.131530528_131530529=	NC_000023.10:g.131530528_131530529del
MBNL3 RefSeqGene	NG_016324.2:g.98468_98469=	NG_016324.2:g.98468_98469del
MBNL3 transcript variant 3	NM_001170701.1:c.193-4166=	NM_001170701.1:c.193-4167_193-4166del
MBNL3 transcript variant 3	NM_001170701.3:c.55-4166=	NM_001170701.3:c.55-4167_55-4166del
MBNL3 transcript variant 4	NM_001170702.1:c.193-4166=	NM_001170702.1:c.193-4167_193-4166del
MBNL3 transcript variant 4	NM_001170702.3:c.55-4166=	NM_001170702.3:c.55-4167_55-4166del
MBNL3 transcript variant 5	NM_001170703.1:c.55-4166=	NM_001170703.1:c.55-4167_55-4166del
MBNL3 transcript variant 5	NM_001170703.2:c.55-4166=	NM_001170703.2:c.55-4167_55-4166del
MBNL3 transcript variant 6	NM_001170704.1:c.55-4166=	NM_001170704.1:c.55-4167_55-4166del
MBNL3 transcript variant 6	NM_001170704.2:c.55-4166=	NM_001170704.2:c.55-4167_55-4166del
MBNL3 transcript variant 7	NM_001386889.1:c.343-4166=	NM_001386889.1:c.343-4167_343-4166del
MBNL3 transcript variant 8	NM_001386891.1:c.343-4166=	NM_001386891.1:c.343-4167_343-4166del
MBNL3 transcript variant 9	NM_001386892.1:c.343-4166=	NM_001386892.1:c.343-4167_343-4166del
MBNL3 transcript variant 10	NM_001386894.1:c.343-4166=	NM_001386894.1:c.343-4167_343-4166del
MBNL3 transcript variant 11	NM_001386896.1:c.343-4166=	NM_001386896.1:c.343-4167_343-4166del
MBNL3 transcript variant 12	NM_001386897.1:c.343-4166=	NM_001386897.1:c.343-4167_343-4166del
MBNL3 transcript variant 13	NM_001386898.1:c.343-4166=	NM_001386898.1:c.343-4167_343-4166del
MBNL3 transcript variant 14	NM_001386899.1:c.343-4166=	NM_001386899.1:c.343-4167_343-4166del
MBNL3 transcript variant 15	NM_001386900.1:c.55-4166=	NM_001386900.1:c.55-4167_55-4166del
MBNL3 transcript variant 16	NM_001386901.1:c.55-4166=	NM_001386901.1:c.55-4167_55-4166del
MBNL3 transcript variant 17	NM_001386902.1:c.55-4166=	NM_001386902.1:c.55-4167_55-4166del
MBNL3 transcript variant 18	NM_001386907.1:c.55-4166=	NM_001386907.1:c.55-4167_55-4166del
MBNL3 transcript variant 19	NM_001386909.1:c.55-4166=	NM_001386909.1:c.55-4167_55-4166del
MBNL3 transcript variant 20	NM_001386910.1:c.55-4166=	NM_001386910.1:c.55-4167_55-4166del
MBNL3 transcript variant 21	NM_001386911.1:c.55-4166=	NM_001386911.1:c.55-4167_55-4166del
MBNL3 transcript variant 22	NM_001386912.1:c.55-4166=	NM_001386912.1:c.55-4167_55-4166del
MBNL3 transcript variant 23	NM_001386913.1:c.55-4166=	NM_001386913.1:c.55-4167_55-4166del
MBNL3 transcript variant 24	NM_001386914.1:c.55-4166=	NM_001386914.1:c.55-4167_55-4166del
MBNL3 transcript variant 25	NM_001386915.1:c.55-4166=	NM_001386915.1:c.55-4167_55-4166del
MBNL3 transcript variant 26	NM_001386916.1:c.-12-4166=	NM_001386916.1:c.-12-4167_-12-4166del
MBNL3 transcript variant 27	NM_001386917.1:c.55-4166=	NM_001386917.1:c.55-4167_55-4166del
MBNL3 transcript variant 28	NM_001386918.1:c.55-4166=	NM_001386918.1:c.55-4167_55-4166del
MBNL3 transcript variant 1	NM_018388.3:c.343-4166=	NM_018388.3:c.343-4167_343-4166del
MBNL3 transcript variant 1	NM_018388.4:c.343-4166=	NM_018388.4:c.343-4167_343-4166del
MBNL3 transcript variant 2	NM_133486.2:c.343-4166=	NM_133486.2:c.343-4167_343-4166del
MBNL3 transcript variant 2	NM_133486.4:c.343-4166=	NM_133486.4:c.343-4167_343-4166del
MBNL3 transcript variant X1	XM_005262431.1:c.343-4166=	XM_005262431.1:c.343-4167_343-4166del
MBNL3 transcript variant X4	XM_005262432.1:c.343-4166=	XM_005262432.1:c.343-4167_343-4166del
MBNL3 transcript variant X5	XM_005262433.1:c.343-4166=	XM_005262433.1:c.343-4167_343-4166del
MBNL3 transcript variant X4	XM_005262434.1:c.343-4166=	XM_005262434.1:c.343-4167_343-4166del
MBNL3 transcript variant X7	XM_005262435.1:c.343-4166=	XM_005262435.1:c.343-4167_343-4166del
MBNL3 transcript variant X6	XM_005262436.1:c.217-4166=	XM_005262436.1:c.217-4167_217-4166del
MBNL3 transcript variant X7	XM_005262437.1:c.193-4166=	XM_005262437.1:c.193-4167_193-4166del
MBNL3 transcript variant X8	XM_005262438.1:c.193-4166=	XM_005262438.1:c.193-4167_193-4166del
MBNL3 transcript variant X9	XM_005262439.1:c.55-4166=	XM_005262439.1:c.55-4167_55-4166del
MBNL3 transcript variant X10	XM_005262440.1:c.55-4166=	XM_005262440.1:c.55-4167_55-4166del
MBNL3 transcript variant X11	XM_005262441.1:c.55-4166=	XM_005262441.1:c.55-4167_55-4166del
MBNL3 transcript variant X12	XM_005262442.1:c.55-4166=	XM_005262442.1:c.55-4167_55-4166del
MBNL3 transcript variant X2	XM_024452403.2:c.217-4166=	XM_024452403.2:c.217-4167_217-4166del
MBNL3 transcript variant X1	XM_047442250.1:c.178-4166=	XM_047442250.1:c.178-4167_178-4166del
MBNL3 transcript variant X3	XM_047442251.1:c.169-4166=	XM_047442251.1:c.169-4167_169-4166del

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, 2 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	GNOMAD	ss4378862995	Apr 26, 2021 (155)
2	1000G_HIGH_COVERAGE	ss5313974633	Oct 17, 2022 (156)
3	HUGCELL_USP	ss5505375138	Oct 17, 2022 (156)
4	SANFORD_IMAGENETICS	ss5665907814	Oct 17, 2022 (156)
5	gnomAD - Genomes	NC_000023.11 - 132396500	Apr 26, 2021 (155)
6	ALFA	NC_000023.11 - 132396500	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
ss5665907814	NC_000023.10:131530527:CT:	NC_000023.11:132396499:CT:
591698021, 4457793221, ss4378862995, ss5313974633, ss5505375138	NC_000023.11:132396499:CT:	NC_000023.11:132396499:CT:	(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 rs1491521915

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

rs1491521915