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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.

rs1491064578

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr2:235784616-235784617 (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
delAC
Variation Type
Deletion
Frequency
delAC=0.000125 (17/135814, GnomAD)
delAC=0.00017 (2/11862, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
AGAP1 : Intron Variant
LOC105373942 : 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 AC=0.99983 =0.00017 0.999663 0.0 0.000337 0
European Sub 7618 AC=0.9997 =0.0003 0.999475 0.0 0.000525 0
African Sub 2816 AC=1.0000 =0.0000 1.0 0.0 0.0 N/A
African Others Sub 108 AC=1.000 =0.000 1.0 0.0 0.0 N/A
African American Sub 2708 AC=1.0000 =0.0000 1.0 0.0 0.0 N/A
Asian Sub 108 AC=1.000 =0.000 1.0 0.0 0.0 N/A
East Asian Sub 84 AC=1.00 =0.00 1.0 0.0 0.0 N/A
Other Asian Sub 24 AC=1.00 =0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 AC=1.000 =0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 AC=1.000 =0.000 1.0 0.0 0.0 N/A
South Asian Sub 94 AC=1.00 =0.00 1.0 0.0 0.0 N/A
Other Sub 470 AC=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 135814 AC=0.999875 delAC=0.000125
gnomAD - Genomes European Sub 73416 AC=0.99982 delAC=0.00018
gnomAD - Genomes African Sub 41130 AC=0.99995 delAC=0.00005
gnomAD - Genomes American Sub 12950 AC=1.00000 delAC=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3258 AC=1.0000 delAC=0.0000
gnomAD - Genomes East Asian Sub 2986 AC=0.9993 delAC=0.0007
gnomAD - Genomes Other Sub 2074 AC=1.0000 delAC=0.0000
Allele Frequency Aggregator Total Global 11862 AC=0.99983 delAC=0.00017
Allele Frequency Aggregator European Sub 7618 AC=0.9997 delAC=0.0003
Allele Frequency Aggregator African Sub 2816 AC=1.0000 delAC=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 AC=1.000 delAC=0.000
Allele Frequency Aggregator Other Sub 470 AC=1.000 delAC=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 AC=1.000 delAC=0.000
Allele Frequency Aggregator Asian Sub 108 AC=1.000 delAC=0.000
Allele Frequency Aggregator South Asian Sub 94 AC=1.00 delAC=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 2 NC_000002.12:g.235784616_235784617del
GRCh37.p13 chr 2 NC_000002.11:g.236693260_236693261del
AGAP1 RefSeqGene NG_030314.1:g.295528_295529del
Gene: AGAP1, ArfGAP with GTPase domain, ankyrin repeat and PH domain 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
AGAP1 transcript variant 1 NM_001037131.3:c.674-1314…

NM_001037131.3:c.674-13143_674-13142del

N/A Intron Variant
AGAP1 transcript variant 3 NM_001244888.2:c.674-1314…

NM_001244888.2:c.674-13143_674-13142del

N/A Intron Variant
AGAP1 transcript variant 2 NM_014914.5:c.674-13143_6…

NM_014914.5:c.674-13143_674-13142del

N/A Intron Variant
AGAP1 transcript variant X17 XM_005246059.5:c.686-1314…

XM_005246059.5:c.686-13143_686-13142del

N/A Intron Variant
AGAP1 transcript variant X13 XM_006712234.4:c.686-1314…

XM_006712234.4:c.686-13143_686-13142del

N/A Intron Variant
AGAP1 transcript variant X14 XM_006712235.4:c.674-1314…

XM_006712235.4:c.674-13143_674-13142del

N/A Intron Variant
AGAP1 transcript variant X2 XM_006712237.4:c.1469-131…

XM_006712237.4:c.1469-13143_1469-13142del

N/A Intron Variant
AGAP1 transcript variant X1 XM_006712239.4:c.1481-131…

XM_006712239.4:c.1481-13143_1481-13142del

N/A Intron Variant
AGAP1 transcript variant X3 XM_011510547.3:c.1481-131…

XM_011510547.3:c.1481-13143_1481-13142del

N/A Intron Variant
AGAP1 transcript variant X7 XM_011510548.3:c.1481-131…

XM_011510548.3:c.1481-13143_1481-13142del

N/A Intron Variant
AGAP1 transcript variant X10 XM_011510549.3:c.1481-131…

XM_011510549.3:c.1481-13143_1481-13142del

N/A Intron Variant
AGAP1 transcript variant X5 XM_017003282.2:c.1346-131…

XM_017003282.2:c.1346-13143_1346-13142del

N/A Intron Variant
AGAP1 transcript variant X8 XM_024452672.2:c.1469-131…

XM_024452672.2:c.1469-13143_1469-13142del

N/A Intron Variant
AGAP1 transcript variant X15 XM_024452676.2:c.1481-131…

XM_024452676.2:c.1481-13143_1481-13142del

N/A Intron Variant
AGAP1 transcript variant X20 XM_024452678.2:c.1481-131…

XM_024452678.2:c.1481-13143_1481-13142del

N/A Intron Variant
AGAP1 transcript variant X22 XM_024452679.2:c.1481-131…

XM_024452679.2:c.1481-13143_1481-13142del

N/A Intron Variant
AGAP1 transcript variant X4 XM_047443190.1:c.1469-131…

XM_047443190.1:c.1469-13143_1469-13142del

N/A Intron Variant
AGAP1 transcript variant X6 XM_047443191.1:c.1334-131…

XM_047443191.1:c.1334-13143_1334-13142del

N/A Intron Variant
AGAP1 transcript variant X9 XM_047443192.1:c.1346-131…

XM_047443192.1:c.1346-13143_1346-13142del

N/A Intron Variant
AGAP1 transcript variant X11 XM_047443193.1:c.1469-131…

XM_047443193.1:c.1469-13143_1469-13142del

N/A Intron Variant
AGAP1 transcript variant X12 XM_047443194.1:c.1346-131…

XM_047443194.1:c.1346-13143_1346-13142del

N/A Intron Variant
AGAP1 transcript variant X16 XM_047443195.1:c.539-1314…

XM_047443195.1:c.539-13143_539-13142del

N/A Intron Variant
AGAP1 transcript variant X18 XM_047443196.1:c.1469-131…

XM_047443196.1:c.1469-13143_1469-13142del

N/A Intron Variant
AGAP1 transcript variant X19 XM_047443197.1:c.539-1314…

XM_047443197.1:c.539-13143_539-13142del

N/A Intron Variant
AGAP1 transcript variant X21 XM_047443200.1:c.1469-131…

XM_047443200.1:c.1469-13143_1469-13142del

N/A Intron Variant
AGAP1 transcript variant X23 XM_047443201.1:c.1334-131…

XM_047443201.1:c.1334-13143_1334-13142del

N/A Intron Variant
Gene: LOC105373942, uncharacterized LOC105373942 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC105373942 transcript variant X2 XR_001739943.3:n. N/A Intron Variant
LOC105373942 transcript variant X1 XR_001739944.2:n. N/A Intron 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 AC= delAC
GRCh38.p14 chr 2 NC_000002.12:g.235784616_235784617= NC_000002.12:g.235784616_235784617del
GRCh37.p13 chr 2 NC_000002.11:g.236693260_236693261= NC_000002.11:g.236693260_236693261del
AGAP1 RefSeqGene NG_030314.1:g.295528_295529= NG_030314.1:g.295528_295529del
AGAP1 transcript variant 1 NM_001037131.2:c.674-13143= NM_001037131.2:c.674-13143_674-13142del
AGAP1 transcript variant 1 NM_001037131.3:c.674-13143= NM_001037131.3:c.674-13143_674-13142del
AGAP1 transcript variant 3 NM_001244888.1:c.674-13143= NM_001244888.1:c.674-13143_674-13142del
AGAP1 transcript variant 3 NM_001244888.2:c.674-13143= NM_001244888.2:c.674-13143_674-13142del
AGAP1 transcript variant 2 NM_014914.4:c.674-13143= NM_014914.4:c.674-13143_674-13142del
AGAP1 transcript variant 2 NM_014914.5:c.674-13143= NM_014914.5:c.674-13143_674-13142del
AGAP1 transcript variant X1 XM_005246058.1:c.686-13143= XM_005246058.1:c.686-13143_686-13142del
AGAP1 transcript variant X2 XM_005246059.1:c.686-13143= XM_005246059.1:c.686-13143_686-13142del
AGAP1 transcript variant X17 XM_005246059.5:c.686-13143= XM_005246059.5:c.686-13143_686-13142del
AGAP1 transcript variant X3 XM_005246060.1:c.272-13143= XM_005246060.1:c.272-13143_272-13142del
AGAP1 transcript variant X4 XM_005246061.1:c.272-13143= XM_005246061.1:c.272-13143_272-13142del
AGAP1 transcript variant X5 XM_005246062.1:c.272-13143= XM_005246062.1:c.272-13143_272-13142del
AGAP1 transcript variant X6 XM_005246063.1:c.374-13143= XM_005246063.1:c.374-13143_374-13142del
AGAP1 transcript variant X7 XM_005246064.1:c.374-13143= XM_005246064.1:c.374-13143_374-13142del
AGAP1 transcript variant X13 XM_006712234.4:c.686-13143= XM_006712234.4:c.686-13143_686-13142del
AGAP1 transcript variant X14 XM_006712235.4:c.674-13143= XM_006712235.4:c.674-13143_674-13142del
AGAP1 transcript variant X2 XM_006712237.4:c.1469-13143= XM_006712237.4:c.1469-13143_1469-13142del
AGAP1 transcript variant X1 XM_006712239.4:c.1481-13143= XM_006712239.4:c.1481-13143_1481-13142del
AGAP1 transcript variant X3 XM_011510547.3:c.1481-13143= XM_011510547.3:c.1481-13143_1481-13142del
AGAP1 transcript variant X7 XM_011510548.3:c.1481-13143= XM_011510548.3:c.1481-13143_1481-13142del
AGAP1 transcript variant X10 XM_011510549.3:c.1481-13143= XM_011510549.3:c.1481-13143_1481-13142del
AGAP1 transcript variant X5 XM_017003282.2:c.1346-13143= XM_017003282.2:c.1346-13143_1346-13142del
AGAP1 transcript variant X8 XM_024452672.2:c.1469-13143= XM_024452672.2:c.1469-13143_1469-13142del
AGAP1 transcript variant X15 XM_024452676.2:c.1481-13143= XM_024452676.2:c.1481-13143_1481-13142del
AGAP1 transcript variant X20 XM_024452678.2:c.1481-13143= XM_024452678.2:c.1481-13143_1481-13142del
AGAP1 transcript variant X22 XM_024452679.2:c.1481-13143= XM_024452679.2:c.1481-13143_1481-13142del
AGAP1 transcript variant X4 XM_047443190.1:c.1469-13143= XM_047443190.1:c.1469-13143_1469-13142del
AGAP1 transcript variant X6 XM_047443191.1:c.1334-13143= XM_047443191.1:c.1334-13143_1334-13142del
AGAP1 transcript variant X9 XM_047443192.1:c.1346-13143= XM_047443192.1:c.1346-13143_1346-13142del
AGAP1 transcript variant X11 XM_047443193.1:c.1469-13143= XM_047443193.1:c.1469-13143_1469-13142del
AGAP1 transcript variant X12 XM_047443194.1:c.1346-13143= XM_047443194.1:c.1346-13143_1346-13142del
AGAP1 transcript variant X16 XM_047443195.1:c.539-13143= XM_047443195.1:c.539-13143_539-13142del
AGAP1 transcript variant X18 XM_047443196.1:c.1469-13143= XM_047443196.1:c.1469-13143_1469-13142del
AGAP1 transcript variant X19 XM_047443197.1:c.539-13143= XM_047443197.1:c.539-13143_539-13142del
AGAP1 transcript variant X21 XM_047443200.1:c.1469-13143= XM_047443200.1:c.1469-13143_1469-13142del
AGAP1 transcript variant X23 XM_047443201.1:c.1334-13143= XM_047443201.1:c.1334-13143_1334-13142del
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#.

1 SubSNP, 2 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss4063453326 Apr 26, 2021 (155)
2 gnomAD - Genomes NC_000002.12 - 235784616 Apr 26, 2021 (155)
3 ALFA NC_000002.12 - 235784616 Apr 26, 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
94903097, 3822396586, ss4063453326 NC_000002.12:235784615:AC: NC_000002.12:235784615:AC: (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 rs1491064578

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