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dbSNP Short Genetic Variations

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.

rs1491376316

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr17:68437948-68437949 (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
Variation Type
Deletion
Frequency
delTA=0.00004 (2/54436, GnomAD)
delTA=0.00000 (0/11862, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
PRKAR1A : Intron Variant
ARSG : Intron Variant
WIPI1 : 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 TA=1.00000 =0.00000 1.0 0.0 0.0 N/A
European Sub 7618 TA=1.0000 =0.0000 1.0 0.0 0.0 N/A
African Sub 2816 TA=1.0000 =0.0000 1.0 0.0 0.0 N/A
African Others Sub 108 TA=1.000 =0.000 1.0 0.0 0.0 N/A
African American Sub 2708 TA=1.0000 =0.0000 1.0 0.0 0.0 N/A
Asian Sub 108 TA=1.000 =0.000 1.0 0.0 0.0 N/A
East Asian Sub 84 TA=1.00 =0.00 1.0 0.0 0.0 N/A
Other Asian Sub 24 TA=1.00 =0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 TA=1.000 =0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 TA=1.000 =0.000 1.0 0.0 0.0 N/A
South Asian Sub 94 TA=1.00 =0.00 1.0 0.0 0.0 N/A
Other Sub 470 TA=1.000 =0.000 1.0 0.0 0.0 N/A


Help

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 54436 TA=0.99996 delTA=0.00004
gnomAD - Genomes European Sub 32296 TA=0.99994 delTA=0.00006
gnomAD - Genomes African Sub 13844 TA=1.00000 delTA=0.00000
gnomAD - Genomes American Sub 4084 TA=1.0000 delTA=0.0000
gnomAD - Genomes East Asian Sub 1898 TA=1.0000 delTA=0.0000
gnomAD - Genomes Ashkenazi Jewish Sub 1586 TA=1.0000 delTA=0.0000
gnomAD - Genomes Other Sub 728 TA=1.000 delTA=0.000
Allele Frequency Aggregator Total Global 11862 TA=1.00000 delTA=0.00000
Allele Frequency Aggregator European Sub 7618 TA=1.0000 delTA=0.0000
Allele Frequency Aggregator African Sub 2816 TA=1.0000 delTA=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 TA=1.000 delTA=0.000
Allele Frequency Aggregator Other Sub 470 TA=1.000 delTA=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 TA=1.000 delTA=0.000
Allele Frequency Aggregator Asian Sub 108 TA=1.000 delTA=0.000
Allele Frequency Aggregator South Asian Sub 94 TA=1.00 delTA=0.00
Help

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.68437948_68437949del
GRCh37.p13 chr 17 NC_000017.10:g.66434089_66434090del
PRKAR1A RefSeqGene (LRG_514) NG_007093.3:g.29326_29327del
ARSG RefSeqGene NG_032814.2:g.183860_183861del
Gene: PRKAR1A, protein kinase cAMP-dependent type I regulatory subunit alpha (plus strand)
Molecule type Change Amino acid[Codon] SO Term
PRKAR1A transcript variant 6 NM_001278433.2:c.-7+24153…

NM_001278433.2:c.-7+24153_-7+24154del

N/A Intron Variant
PRKAR1A transcript variant 4 NM_001276289.2:c. N/A Genic Upstream Transcript Variant
PRKAR1A transcript variant 5 NM_001276290.1:c. N/A Genic Upstream Transcript Variant
PRKAR1A transcript variant 7 NM_001369389.1:c. N/A Genic Upstream Transcript Variant
PRKAR1A transcript variant 8 NM_001369390.1:c. N/A Genic Upstream Transcript Variant
PRKAR1A transcript variant 1 NM_002734.5:c. N/A Genic Upstream Transcript Variant
PRKAR1A transcript variant 2 NM_212471.3:c. N/A Genic Upstream Transcript Variant
PRKAR1A transcript variant 3 NM_212472.2:c. N/A Genic Upstream Transcript Variant
PRKAR1A transcript variant X1 XM_011524984.4:c. N/A Genic Upstream Transcript Variant
PRKAR1A transcript variant X2 XM_047436369.1:c. N/A Genic Upstream Transcript Variant
PRKAR1A transcript variant X3 XM_047436370.1:c. N/A Genic Upstream Transcript Variant
Gene: WIPI1, WD repeat domain, phosphoinositide interacting 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
WIPI1 transcript variant 2 NM_001320772.2:c.185-1470…

NM_001320772.2:c.185-1470_185-1469del

N/A Intron Variant
WIPI1 transcript variant 1 NM_017983.7:c.431-1470_43…

NM_017983.7:c.431-1470_431-1469del

N/A Intron Variant
WIPI1 transcript variant 3 NR_135470.2:n. N/A Intron Variant
WIPI1 transcript variant 4 NR_135471.2:n. N/A Intron Variant
WIPI1 transcript variant X1 XM_017024808.2:c.47-1470_…

XM_017024808.2:c.47-1470_47-1469del

N/A Intron Variant
Gene: ARSG, arylsulfatase G (plus strand)
Molecule type Change Amino acid[Codon] SO Term
ARSG transcript variant 9 NM_001352905.2:c.*44-2753…

NM_001352905.2:c.*44-2753_*44-2752del

N/A Intron Variant
ARSG transcript variant 12 NM_001352909.2:c.1256-275…

NM_001352909.2:c.1256-2753_1256-2752del

N/A Intron Variant
ARSG transcript variant 13 NM_001352910.2:c.1304-275…

NM_001352910.2:c.1304-2753_1304-2752del

N/A Intron Variant
ARSG transcript variant 2 NM_001267727.2:c. N/A Genic Downstream Transcript Variant
ARSG transcript variant 3 NM_001352899.2:c. N/A Genic Downstream Transcript Variant
ARSG transcript variant 4 NM_001352900.2:c. N/A Genic Downstream Transcript Variant
ARSG transcript variant 5 NM_001352901.2:c. N/A Genic Downstream Transcript Variant
ARSG transcript variant 6 NM_001352902.2:c. N/A Genic Downstream Transcript Variant
ARSG transcript variant 7 NM_001352903.2:c. N/A Genic Downstream Transcript Variant
ARSG transcript variant 8 NM_001352904.2:c. N/A Genic Downstream Transcript Variant
ARSG transcript variant 10 NM_001352906.2:c. N/A Genic Downstream Transcript Variant
ARSG transcript variant 11 NM_001352907.2:c. N/A Genic Downstream Transcript Variant
ARSG transcript variant 1 NM_014960.5:c. N/A Genic Downstream Transcript Variant
ARSG transcript variant X6 XM_047435634.1:c.*44-2753…

XM_047435634.1:c.*44-2753_*44-2752del

N/A Intron Variant
ARSG transcript variant X9 XM_047435637.1:c.1385-275…

XM_047435637.1:c.1385-2753_1385-2752del

N/A Intron Variant
ARSG transcript variant X15 XM_047435642.1:c.1183-275…

XM_047435642.1:c.1183-2753_1183-2752del

N/A Intron Variant
ARSG transcript variant X16 XM_047435643.1:c.1183-275…

XM_047435643.1:c.1183-2753_1183-2752del

N/A Intron Variant
ARSG transcript variant X17 XM_047435644.1:c.1304-275…

XM_047435644.1:c.1304-2753_1304-2752del

N/A Intron Variant
ARSG transcript variant X18 XM_047435645.1:c.1304-275…

XM_047435645.1:c.1304-2753_1304-2752del

N/A Intron Variant
ARSG transcript variant X19 XM_047435646.1:c.1304-275…

XM_047435646.1:c.1304-2753_1304-2752del

N/A Intron Variant
ARSG transcript variant X22 XM_047435647.1:c.1183-275…

XM_047435647.1:c.1183-2753_1183-2752del

N/A Intron Variant
ARSG transcript variant X1 XM_011524536.3:c. N/A Genic Downstream Transcript Variant
ARSG transcript variant X4 XM_011524537.2:c. N/A Genic Downstream Transcript Variant
ARSG transcript variant X28 XM_011524546.3:c. N/A Genic Downstream Transcript Variant
ARSG transcript variant X3 XM_017024360.3:c. N/A Genic Downstream Transcript Variant
ARSG transcript variant X13 XM_017024365.2:c. N/A Genic Downstream Transcript Variant
ARSG transcript variant X20 XM_017024368.2:c. N/A Genic Downstream Transcript Variant
ARSG transcript variant X2 XM_047435632.1:c. N/A Genic Downstream Transcript Variant
ARSG transcript variant X5 XM_047435633.1:c. N/A Genic Downstream Transcript Variant
ARSG transcript variant X7 XM_047435635.1:c. N/A Genic Downstream Transcript Variant
ARSG transcript variant X8 XM_047435636.1:c. N/A Genic Downstream Transcript Variant
ARSG transcript variant X10 XM_047435638.1:c. N/A Genic Downstream Transcript Variant
ARSG transcript variant X11 XM_047435639.1:c. N/A Genic Downstream Transcript Variant
ARSG transcript variant X12 XM_047435640.1:c. N/A Genic Downstream Transcript Variant
ARSG transcript variant X14 XM_047435641.1:c. N/A Genic Downstream Transcript Variant
ARSG transcript variant X23 XM_047435648.1:c. N/A Genic Downstream Transcript Variant
ARSG transcript variant X24 XM_047435649.1:c. N/A Genic Downstream Transcript Variant
ARSG transcript variant X25 XM_047435650.1:c. N/A Genic Downstream Transcript Variant
ARSG transcript variant X26 XM_047435651.1:c. N/A Genic Downstream Transcript Variant
ARSG transcript variant X27 XM_047435652.1:c. N/A Genic Downstream Transcript Variant
ARSG transcript variant X29 XM_047435653.1:c. N/A Genic Downstream Transcript Variant
ARSG transcript variant X30 XM_047435654.1:c. N/A Genic Downstream Transcript Variant
ARSG transcript variant X31 XM_047435655.1:c. N/A Genic Downstream Transcript Variant
ARSG transcript variant X21 XR_007065287.1:n. N/A Genic Downstream Transcript Variant
Help

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
Help

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= delTA
GRCh38.p14 chr 17 NC_000017.11:g.68437948_68437949= NC_000017.11:g.68437948_68437949del
GRCh37.p13 chr 17 NC_000017.10:g.66434089_66434090= NC_000017.10:g.66434089_66434090del
PRKAR1A RefSeqGene (LRG_514) NG_007093.3:g.29326_29327= NG_007093.3:g.29326_29327del
ARSG RefSeqGene NG_032814.2:g.183860_183861= NG_032814.2:g.183860_183861del
PRKAR1A transcript variant 6 NM_001278433.2:c.-7+24153= NM_001278433.2:c.-7+24153_-7+24154del
WIPI1 transcript variant 2 NM_001320772.2:c.185-1469= NM_001320772.2:c.185-1470_185-1469del
ARSG transcript variant 9 NM_001352905.2:c.*44-2753= NM_001352905.2:c.*44-2753_*44-2752del
ARSG transcript variant 12 NM_001352909.2:c.1256-2753= NM_001352909.2:c.1256-2753_1256-2752del
ARSG transcript variant 13 NM_001352910.2:c.1304-2753= NM_001352910.2:c.1304-2753_1304-2752del
WIPI1 transcript NM_017983.5:c.431-1469= NM_017983.5:c.431-1470_431-1469del
WIPI1 transcript variant 1 NM_017983.7:c.431-1469= NM_017983.7:c.431-1470_431-1469del
WIPI1 transcript variant X1 XM_005257497.1:c.185-1469= XM_005257497.1:c.185-1470_185-1469del
WIPI1 transcript variant X1 XM_017024808.2:c.47-1469= XM_017024808.2:c.47-1470_47-1469del
ARSG transcript variant X6 XM_047435634.1:c.*44-2753= XM_047435634.1:c.*44-2753_*44-2752del
ARSG transcript variant X9 XM_047435637.1:c.1385-2753= XM_047435637.1:c.1385-2753_1385-2752del
ARSG transcript variant X15 XM_047435642.1:c.1183-2753= XM_047435642.1:c.1183-2753_1183-2752del
ARSG transcript variant X16 XM_047435643.1:c.1183-2753= XM_047435643.1:c.1183-2753_1183-2752del
ARSG transcript variant X17 XM_047435644.1:c.1304-2753= XM_047435644.1:c.1304-2753_1304-2752del
ARSG transcript variant X18 XM_047435645.1:c.1304-2753= XM_047435645.1:c.1304-2753_1304-2752del
ARSG transcript variant X19 XM_047435646.1:c.1304-2753= XM_047435646.1:c.1304-2753_1304-2752del
ARSG transcript variant X22 XM_047435647.1:c.1183-2753= XM_047435647.1:c.1183-2753_1183-2752del
Help

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#.

2 SubSNP, 2 Frequency submissions
No Submitter Submission ID Date (Build)
1 EVA_DECODE ss3700813992 Jul 13, 2019 (153)
2 GNOMAD ss4314811081 Apr 27, 2021 (155)
3 gnomAD - Genomes NC_000017.11 - 68437948 Apr 27, 2021 (155)
4 ALFA NC_000017.11 - 68437948 Apr 27, 2021 (155)
Help

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
512447643, 13530254217, ss3700813992, ss4314811081 NC_000017.11:68437947:TA: NC_000017.11:68437947:TA: (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs1491376316

Help

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.

Software version is: 2.0.1.post820+afb47a3d