Name: rs1487767969
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.

rs1487767969

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr17:48307400 (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: G>A / G>C / G>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.000014 (2/140278, GnomAD)
A=0.00000 (0/14044, ALFA)
C=0.00000 (0/14044, ALFA) (+ 5 more)
T=0.00000 (0/14044, ALFA)
A=0.0002 (1/6404, 1000G_30x)
T=0.0002 (1/6404, 1000G_30x)
G=0.5 (1/2, SGDP_PRJ)
A=0.5 (1/2, SGDP_PRJ)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: SKAP1-AS2 : Non Coding Transcript Variant
SKAP1 : 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	14044	G=1.00000	A=0.00000, C=0.00000, T=0.00000	1.0	N/A
European	Sub	9690	G=1.0000	A=0.0000, C=0.0000, T=0.0000	1.0	N/A
African	Sub	2896	G=1.0000	A=0.0000, C=0.0000, T=0.0000	1.0	N/A
African Others	Sub	114	G=1.000	A=0.000, C=0.000, T=0.000	1.0	N/A
African American	Sub	2782	G=1.0000	A=0.0000, C=0.0000, T=0.0000	1.0	N/A
Asian	Sub	112	G=1.000	A=0.000, C=0.000, T=0.000	1.0	N/A
East Asian	Sub	86	G=1.00	A=0.00, C=0.00, T=0.00	1.0	N/A
Other Asian	Sub	26	G=1.00	A=0.00, C=0.00, T=0.00	1.0	N/A
Latin American 1	Sub	146	G=1.000	A=0.000, C=0.000, T=0.000	1.0	N/A
Latin American 2	Sub	610	G=1.000	A=0.000, C=0.000, T=0.000	1.0	N/A
South Asian	Sub	96	G=1.00	A=0.00, C=0.00, T=0.00	1.0	N/A
Other	Sub	494	G=1.000	A=0.000, C=0.000, T=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 - Genomes	Global	Study-wide	140278	G=0.999986	T=0.000014
gnomAD - Genomes	European	Sub	75960	G=1.00000	T=0.00000
gnomAD - Genomes	African	Sub	42054	G=0.99995	T=0.00005
gnomAD - Genomes	American	Sub	13656	G=1.00000	T=0.00000
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	G=1.0000	T=0.0000
gnomAD - Genomes	East Asian	Sub	3134	G=1.0000	T=0.0000
gnomAD - Genomes	Other	Sub	2150	G=1.0000	T=0.0000
Allele Frequency Aggregator	Total	Global	14044	G=1.00000	A=0.00000, C=0.00000, T=0.00000
Allele Frequency Aggregator	European	Sub	9690	G=1.0000	A=0.0000, C=0.0000, T=0.0000
Allele Frequency Aggregator	African	Sub	2896	G=1.0000	A=0.0000, C=0.0000, T=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	610	G=1.000	A=0.000, C=0.000, T=0.000
Allele Frequency Aggregator	Other	Sub	494	G=1.000	A=0.000, C=0.000, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	G=1.000	A=0.000, C=0.000, T=0.000
Allele Frequency Aggregator	Asian	Sub	112	G=1.000	A=0.000, C=0.000, T=0.000
Allele Frequency Aggregator	South Asian	Sub	96	G=1.00	A=0.00, C=0.00, T=0.00
1000Genomes_30x	Global	Study-wide	6404	G=0.9997	A=0.0002, T=0.0002
1000Genomes_30x	African	Sub	1786	G=0.9989	A=0.0006, T=0.0006
1000Genomes_30x	Europe	Sub	1266	G=1.0000	A=0.0000, T=0.0000
1000Genomes_30x	South Asian	Sub	1202	G=1.0000	A=0.0000, T=0.0000
1000Genomes_30x	East Asian	Sub	1170	G=1.0000	A=0.0000, T=0.0000
1000Genomes_30x	American	Sub	980	G=1.000	A=0.000, T=0.000
SGDP_PRJ	Global	Study-wide	2	G=0.5	A=0.5

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.48307400G>A
GRCh38.p14 chr 17	NC_000017.11:g.48307400G>C
GRCh38.p14 chr 17	NC_000017.11:g.48307400G>T
GRCh37.p13 chr 17	NC_000017.10:g.46384762G>A
GRCh37.p13 chr 17	NC_000017.10:g.46384762G>C
GRCh37.p13 chr 17	NC_000017.10:g.46384762G>T

Gene: SKAP1, src kinase associated phosphoprotein 1 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SKAP1 transcript variant 2	NM_001075099.2:c.280+3850… NM_001075099.2:c.280+38505C>T	N/A	Intron Variant
SKAP1 transcript variant 1	NM_003726.4:c.280+38505C>T	N/A	Intron Variant
SKAP1 transcript variant X6	XM_005257755.5:c.280+3850… XM_005257755.5:c.280+38505C>T	N/A	Intron Variant
SKAP1 transcript variant X1	XM_047436972.1:c.280+3850… XM_047436972.1:c.280+38505C>T	N/A	Intron Variant
SKAP1 transcript variant X2	XM_047436973.1:c.280+3850… XM_047436973.1:c.280+38505C>T	N/A	Intron Variant
SKAP1 transcript variant X3	XM_047436974.1:c.232+3850… XM_047436974.1:c.232+38505C>T	N/A	Intron Variant
SKAP1 transcript variant X4	XM_047436975.1:c.280+3850… XM_047436975.1:c.280+38505C>T	N/A	Intron Variant
SKAP1 transcript variant X5	XM_047436976.1:c.226+3850… XM_047436976.1:c.226+38505C>T	N/A	Intron Variant
SKAP1 transcript variant X7	XM_047436977.1:c.280+3850… XM_047436977.1:c.280+38505C>T	N/A	Intron Variant
SKAP1 transcript variant X9	XM_047436980.1:c.-122+385… XM_047436980.1:c.-122+38505C>T	N/A	Intron Variant
SKAP1 transcript variant X8	XM_017025258.2:c.	N/A	Genic Upstream Transcript Variant
SKAP1 transcript variant X10	XM_047436978.1:c.	N/A	Genic Upstream Transcript Variant
SKAP1 transcript variant X11	XM_047436979.1:c.	N/A	Genic Upstream Transcript Variant

Gene: SKAP1-AS2, SKAP1 antisense RNA 2 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SKAP1-AS2 transcript variant 2	NR_131240.1:n.239G>A	N/A	Non Coding Transcript Variant
SKAP1-AS2 transcript variant 2	NR_131240.1:n.239G>C	N/A	Non Coding Transcript Variant
SKAP1-AS2 transcript variant 2	NR_131240.1:n.239G>T	N/A	Non Coding Transcript Variant
SKAP1-AS2 transcript variant 1	NR_131239.1:n.299G>A	N/A	Non Coding Transcript Variant
SKAP1-AS2 transcript variant 1	NR_131239.1:n.299G>C	N/A	Non Coding Transcript Variant
SKAP1-AS2 transcript variant 1	NR_131239.1:n.299G>T	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	G=	A	C	T
GRCh38.p14 chr 17	NC_000017.11:g.48307400=	NC_000017.11:g.48307400G>A	NC_000017.11:g.48307400G>C	NC_000017.11:g.48307400G>T
GRCh37.p13 chr 17	NC_000017.10:g.46384762=	NC_000017.10:g.46384762G>A	NC_000017.10:g.46384762G>C	NC_000017.10:g.46384762G>T
SKAP1-AS2 transcript variant 1	NR_131239.1:n.299=	NR_131239.1:n.299G>A	NR_131239.1:n.299G>C	NR_131239.1:n.299G>T
SKAP1-AS2 transcript variant 2	NR_131240.1:n.239=	NR_131240.1:n.239G>A	NR_131240.1:n.239G>C	NR_131240.1:n.239G>T
SKAP1 transcript variant 2	NM_001075099.1:c.280+38505=	NM_001075099.1:c.280+38505C>T	NM_001075099.1:c.280+38505C>G	NM_001075099.1:c.280+38505C>A
SKAP1 transcript variant 2	NM_001075099.2:c.280+38505=	NM_001075099.2:c.280+38505C>T	NM_001075099.2:c.280+38505C>G	NM_001075099.2:c.280+38505C>A
SKAP1 transcript variant 1	NM_003726.3:c.280+38505=	NM_003726.3:c.280+38505C>T	NM_003726.3:c.280+38505C>G	NM_003726.3:c.280+38505C>A
SKAP1 transcript variant 1	NM_003726.4:c.280+38505=	NM_003726.4:c.280+38505C>T	NM_003726.4:c.280+38505C>G	NM_003726.4:c.280+38505C>A
SKAP1 transcript variant X1	XM_005257754.1:c.247+38505=	XM_005257754.1:c.247+38505C>T	XM_005257754.1:c.247+38505C>G	XM_005257754.1:c.247+38505C>A
SKAP1 transcript variant X2	XM_005257755.1:c.280+38505=	XM_005257755.1:c.280+38505C>T	XM_005257755.1:c.280+38505C>G	XM_005257755.1:c.280+38505C>A
SKAP1 transcript variant X6	XM_005257755.5:c.280+38505=	XM_005257755.5:c.280+38505C>T	XM_005257755.5:c.280+38505C>G	XM_005257755.5:c.280+38505C>A
SKAP1 transcript variant X3	XM_005257756.1:c.-3+36857=	XM_005257756.1:c.-3+36857C>T	XM_005257756.1:c.-3+36857C>G	XM_005257756.1:c.-3+36857C>A
SKAP1 transcript variant X1	XM_047436972.1:c.280+38505=	XM_047436972.1:c.280+38505C>T	XM_047436972.1:c.280+38505C>G	XM_047436972.1:c.280+38505C>A
SKAP1 transcript variant X2	XM_047436973.1:c.280+38505=	XM_047436973.1:c.280+38505C>T	XM_047436973.1:c.280+38505C>G	XM_047436973.1:c.280+38505C>A
SKAP1 transcript variant X3	XM_047436974.1:c.232+38505=	XM_047436974.1:c.232+38505C>T	XM_047436974.1:c.232+38505C>G	XM_047436974.1:c.232+38505C>A
SKAP1 transcript variant X4	XM_047436975.1:c.280+38505=	XM_047436975.1:c.280+38505C>T	XM_047436975.1:c.280+38505C>G	XM_047436975.1:c.280+38505C>A
SKAP1 transcript variant X5	XM_047436976.1:c.226+38505=	XM_047436976.1:c.226+38505C>T	XM_047436976.1:c.226+38505C>G	XM_047436976.1:c.226+38505C>A
SKAP1 transcript variant X7	XM_047436977.1:c.280+38505=	XM_047436977.1:c.280+38505C>T	XM_047436977.1:c.280+38505C>G	XM_047436977.1:c.280+38505C>A
SKAP1 transcript variant X9	XM_047436980.1:c.-122+38505=	XM_047436980.1:c.-122+38505C>T	XM_047436980.1:c.-122+38505C>G	XM_047436980.1:c.-122+38505C>A

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#.

8 SubSNP, 7 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	GNOMAD	ss2950318493	Nov 08, 2017 (151)
2	SGDP_PRJ	ss3885830112	Apr 27, 2020 (154)
3	TOPMED	ss5037266065	Apr 27, 2021 (155)
4	TOPMED	ss5037266066	Apr 27, 2021 (155)
5	TOPMED	ss5037266067	Apr 27, 2021 (155)
6	EVA	ss5427827674	Oct 16, 2022 (156)
7	1000G_HIGH_COVERAGE	ss5607050638	Oct 16, 2022 (156)
8	EVA	ss5914077062	Oct 16, 2022 (156)
9	1000Genomes_30x	NC_000017.11 - 48307400	Oct 16, 2022 (156)
10	gnomAD - Genomes	NC_000017.11 - 48307400	Apr 27, 2021 (155)
11	SGDP_PRJ	NC_000017.10 - 46384762	Apr 27, 2020 (154)
12	TopMed Submission ignored due to conflicting rows: Row 252811727 (NC_000017.11:48307399:G:A 1/264690) Row 252811728 (NC_000017.11:48307399:G:C 1/264690) Row 252811729 (NC_000017.11:48307399:G:T 14/264690)	-	Apr 27, 2021 (155)
13	TopMed Submission ignored due to conflicting rows: Row 252811727 (NC_000017.11:48307399:G:A 1/264690) Row 252811728 (NC_000017.11:48307399:G:C 1/264690) Row 252811729 (NC_000017.11:48307399:G:T 14/264690)	-	Apr 27, 2021 (155)
14	TopMed Submission ignored due to conflicting rows: Row 252811727 (NC_000017.11:48307399:G:A 1/264690) Row 252811728 (NC_000017.11:48307399:G:C 1/264690) Row 252811729 (NC_000017.11:48307399:G:T 14/264690)	-	Apr 27, 2021 (155)
15	ALFA	NC_000017.11 - 48307400	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
37847092, ss3885830112, ss5427827674	NC_000017.10:46384761:G:A	NC_000017.11:48307399:G:A	(self)
94576573, 10559111318, ss5037266065, ss5607050638, ss5914077062	NC_000017.11:48307399:G:A	NC_000017.11:48307399:G:A	(self)
10559111318, ss5037266066	NC_000017.11:48307399:G:C	NC_000017.11:48307399:G:C	(self)
ss2950318493	NC_000017.10:46384761:G:T	NC_000017.11:48307399:G:T	(self)
94576573, 508370176, 10559111318, ss5037266067, ss5607050638	NC_000017.11:48307399:G:T	NC_000017.11:48307399:G:T	(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 rs1487767969

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs1487767969