Name: rs1442987315
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.

rs1442987315

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr17:19063941-19063943 (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: delCC / dupCC
Variation Type: Indel Insertion and Deletion
Frequency: delCC=0.000011 (2/177468, GnomAD_exome)
dupCC=0.00001 (1/93464, GnomAD)
delCC=0.00001 (1/85090, ExAC) (+ 3 more)
delCC=0.00004 (1/22322, 14KJPN)
delCC=0.00007 (1/14190, 8.3KJPN)
dupCC=0.00000 (0/11860, ALFA)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: SNORD3B-2 : Non Coding Transcript 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	11860	CCC=1.00000	CCCCC=0.00000	1.0	N/A
European	Sub	7616	CCC=1.0000	CCCCC=0.0000	1.0	N/A
African	Sub	2816	CCC=1.0000	CCCCC=0.0000	1.0	N/A
African Others	Sub	108	CCC=1.000	CCCCC=0.000	1.0	N/A
African American	Sub	2708	CCC=1.0000	CCCCC=0.0000	1.0	N/A
Asian	Sub	108	CCC=1.000	CCCCC=0.000	1.0	N/A
East Asian	Sub	84	CCC=1.00	CCCCC=0.00	1.0	N/A
Other Asian	Sub	24	CCC=1.00	CCCCC=0.00	1.0	N/A
Latin American 1	Sub	146	CCC=1.000	CCCCC=0.000	1.0	N/A
Latin American 2	Sub	610	CCC=1.000	CCCCC=0.000	1.0	N/A
South Asian	Sub	94	CCC=1.00	CCCCC=0.00	1.0	N/A
Other	Sub	470	CCC=1.000	CCCCC=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
gnomAD - Exomes	Global	Study-wide	177468	CCC=0.999989	delCC=0.000011
gnomAD - Exomes	European	Sub	111380	CCC=1.000000	delCC=0.000000
gnomAD - Exomes	Asian	Sub	22902	CCC=0.99991	delCC=0.00009
gnomAD - Exomes	American	Sub	21464	CCC=1.00000	delCC=0.00000
gnomAD - Exomes	Ashkenazi Jewish	Sub	9360	CCC=1.0000	delCC=0.0000
gnomAD - Exomes	African	Sub	7212	CCC=1.0000	delCC=0.0000
gnomAD - Exomes	Other	Sub	5150	CCC=1.0000	delCC=0.0000
gnomAD - Genomes	Global	Study-wide	93464	- No frequency provided	dupCC=0.00001
gnomAD - Genomes	European	Sub	67180	- No frequency provided	dupCC=0.00001
gnomAD - Genomes	African	Sub	12594	- No frequency provided	dupCC=0.00000
gnomAD - Genomes	American	Sub	8840	- No frequency provided	dupCC=0.0000
gnomAD - Genomes	Ashkenazi Jewish	Sub	3112	- No frequency provided	dupCC=0.0000
gnomAD - Genomes	Other	Sub	1512	- No frequency provided	dupCC=0.0000
gnomAD - Genomes	East Asian	Sub	226	- No frequency provided	dupCC=0.000
ExAC	Global	Study-wide	85090	CCC=0.99999	delCC=0.00001
ExAC	Europe	Sub	65092	CCC=1.00000	delCC=0.00000
ExAC	Asian	Sub	9534	CCC=0.9999	delCC=0.0001
ExAC	American	Sub	6940	CCC=1.0000	delCC=0.0000
ExAC	African	Sub	2790	CCC=1.0000	delCC=0.0000
ExAC	Other	Sub	734	CCC=1.000	delCC=0.000
14KJPN	JAPANESE	Study-wide	22322	CCC=0.99996	delCC=0.00004
8.3KJPN	JAPANESE	Study-wide	14190	CCC=0.99993	delCC=0.00007
Allele Frequency Aggregator	Total	Global	11860	CCC=1.00000	dupCC=0.00000
Allele Frequency Aggregator	European	Sub	7616	CCC=1.0000	dupCC=0.0000
Allele Frequency Aggregator	African	Sub	2816	CCC=1.0000	dupCC=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	610	CCC=1.000	dupCC=0.000
Allele Frequency Aggregator	Other	Sub	470	CCC=1.000	dupCC=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	CCC=1.000	dupCC=0.000
Allele Frequency Aggregator	Asian	Sub	108	CCC=1.000	dupCC=0.000
Allele Frequency Aggregator	South Asian	Sub	94	CCC=1.00	dupCC=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 17	NC_000017.11:g.19063942_19063943del
GRCh38.p14 chr 17	NC_000017.11:g.19063942_19063943dup
GRCh37.p13 chr 17	NC_000017.10:g.18967255_18967256del
GRCh37.p13 chr 17	NC_000017.10:g.18967255_18967256dup

Gene: SNORD3B-2, small nucleolar RNA, C/D box 3B-2 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SNORD3B-2 transcript	NR_003924.1:n.195_196del	N/A	Non Coding Transcript Variant
SNORD3B-2 transcript	NR_003924.1:n.195_196dup	N/A	Non Coding 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	CCC=	delCC	dupCC
GRCh38.p14 chr 17	NC_000017.11:g.19063941_19063943=	NC_000017.11:g.19063942_19063943del	NC_000017.11:g.19063942_19063943dup
GRCh37.p13 chr 17	NC_000017.10:g.18967254_18967256=	NC_000017.10:g.18967255_18967256del	NC_000017.10:g.18967255_18967256dup
SNORD3B-2 transcript	NR_003924.1:n.194_196=	NR_003924.1:n.195_196del	NR_003924.1:n.195_196dup

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, 6 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	EVA_EXAC	ss1712135129	Jan 10, 2018 (151)
2	GNOMAD	ss4308971718	Apr 26, 2021 (155)
3	TOMMO_GENOMICS	ss5221787307	Apr 26, 2021 (155)
4	TOMMO_GENOMICS	ss5777468692	Oct 17, 2022 (156)
5	ExAC	NC_000017.10 - 18967254	Oct 12, 2018 (152)
6	gnomAD - Genomes	NC_000017.11 - 19063941	Apr 26, 2021 (155)
7	gnomAD - Exomes	NC_000017.10 - 18967254	Jul 13, 2019 (153)
8	8.3KJPN	NC_000017.10 - 18967254	Apr 26, 2021 (155)
9	14KJPN	NC_000017.11 - 19063941	Oct 17, 2022 (156)
10	ALFA	NC_000017.11 - 19063941	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
3093022, 11833487, 79756614, ss1712135129, ss5221787307	NC_000017.10:18967253:CC:	NC_000017.11:19063940:CCC:C	(self)
111305796, ss5777468692	NC_000017.11:19063940:CC:	NC_000017.11:19063940:CCC:C
503205504, ss4308971718	NC_000017.11:19063940::CC	NC_000017.11:19063940:CCC:CCCCC	(self)
9076948941	NC_000017.11:19063940:CCC:CCCCC	NC_000017.11:19063940:CCC:CCCCC	(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 rs1442987315

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

rs1442987315