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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.

rs1491434709

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr19:6138468-6138470 (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
delGG
Variation Type
Indel Insertion and Deletion
Frequency
delGG=0.001413 (162/114640, GnomAD)
delGG=0.00014 (4/28198, 14KJPN)
delGG=0.00034 (4/11862, ALFA) (+ 1 more)
delGG=0.0012 (8/6404, 1000G_30x)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ACSBG2 : Intron Variant
LOC105372255 : 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 GGG=0.99966 G=0.00034 0.999326 0.0 0.000674 0
European Sub 7618 GGG=0.9999 G=0.0001 0.999737 0.0 0.000263 0
African Sub 2816 GGG=0.9993 G=0.0007 0.99858 0.0 0.00142 0
African Others Sub 108 GGG=1.000 G=0.000 1.0 0.0 0.0 N/A
African American Sub 2708 GGG=0.9993 G=0.0007 0.998523 0.0 0.001477 0
Asian Sub 108 GGG=1.000 G=0.000 1.0 0.0 0.0 N/A
East Asian Sub 84 GGG=1.00 G=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 24 GGG=1.00 G=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 GGG=1.000 G=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 GGG=0.998 G=0.002 0.996721 0.0 0.003279 0
South Asian Sub 94 GGG=1.00 G=0.00 1.0 0.0 0.0 N/A
Other Sub 470 GGG=1.000 G=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 114640 GGG=0.998587 delGG=0.001413
gnomAD - Genomes European Sub 63830 GGG=0.99842 delGG=0.00158
gnomAD - Genomes African Sub 33772 GGG=0.99885 delGG=0.00115
gnomAD - Genomes American Sub 9510 GGG=0.9982 delGG=0.0018
gnomAD - Genomes Ashkenazi Jewish Sub 3022 GGG=1.0000 delGG=0.0000
gnomAD - Genomes East Asian Sub 2768 GGG=0.9996 delGG=0.0004
gnomAD - Genomes Other Sub 1738 GGG=0.9977 delGG=0.0023
14KJPN JAPANESE Study-wide 28198 GGG=0.99986 delGG=0.00014
Allele Frequency Aggregator Total Global 11862 GGG=0.99966 delGG=0.00034
Allele Frequency Aggregator European Sub 7618 GGG=0.9999 delGG=0.0001
Allele Frequency Aggregator African Sub 2816 GGG=0.9993 delGG=0.0007
Allele Frequency Aggregator Latin American 2 Sub 610 GGG=0.998 delGG=0.002
Allele Frequency Aggregator Other Sub 470 GGG=1.000 delGG=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 GGG=1.000 delGG=0.000
Allele Frequency Aggregator Asian Sub 108 GGG=1.000 delGG=0.000
Allele Frequency Aggregator South Asian Sub 94 GGG=1.00 delGG=0.00
1000Genomes_30x Global Study-wide 6404 GGG=0.9988 delGG=0.0012
1000Genomes_30x African Sub 1786 GGG=0.9966 delGG=0.0034
1000Genomes_30x Europe Sub 1266 GGG=0.9992 delGG=0.0008
1000Genomes_30x South Asian Sub 1202 GGG=1.0000 delGG=0.0000
1000Genomes_30x East Asian Sub 1170 GGG=0.9991 delGG=0.0009
1000Genomes_30x American Sub 980 GGG=1.000 delGG=0.000
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 19 NC_000019.10:g.6138469_6138470del
GRCh37.p13 chr 19 NC_000019.9:g.6138480_6138481del
Gene: ACSBG2, acyl-CoA synthetase bubblegum family member 2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
ACSBG2 transcript variant 1 NM_001289177.2:c.-32+2551…

NM_001289177.2:c.-32+2551_-32+2552del

N/A Intron Variant
ACSBG2 transcript variant 3 NM_001289178.2:c.-32+2605…

NM_001289178.2:c.-32+2605_-32+2606del

N/A Intron Variant
ACSBG2 transcript variant 4 NM_001289179.2:c.-32+2560…

NM_001289179.2:c.-32+2560_-32+2561del

N/A Intron Variant
ACSBG2 transcript variant 5 NM_001289180.2:c.-472+256…

NM_001289180.2:c.-472+2560_-472+2561del

N/A Intron Variant
ACSBG2 transcript variant 6 NM_001321384.2:c.-172+256…

NM_001321384.2:c.-172+2560_-172+2561del

N/A Intron Variant
ACSBG2 transcript variant 2 NM_030924.5:c.-32+2560_-3…

NM_030924.5:c.-32+2560_-32+2561del

N/A Intron Variant
ACSBG2 transcript variant X4 XM_005259653.4:c.-32+2560…

XM_005259653.4:c.-32+2560_-32+2561del

N/A Intron Variant
ACSBG2 transcript variant X1 XM_017027332.3:c.-32+1054…

XM_017027332.3:c.-32+1054_-32+1055del

N/A Intron Variant
ACSBG2 transcript variant X2 XM_017027333.2:c.-32+2560…

XM_017027333.2:c.-32+2560_-32+2561del

N/A Intron Variant
ACSBG2 transcript variant X3 XM_047439477.1:c.-32+2560…

XM_047439477.1:c.-32+2560_-32+2561del

N/A Intron Variant
ACSBG2 transcript variant X6 XM_011528329.2:c. N/A Genic Upstream Transcript Variant
ACSBG2 transcript variant X5 XM_047439478.1:c. N/A Genic Upstream Transcript Variant
Gene: LOC105372255, uncharacterized LOC105372255 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC105372255 transcript variant X1 XR_936282.3:n. N/A Intron Variant
LOC105372255 transcript variant X3 XR_936283.3:n. N/A Intron Variant
LOC105372255 transcript variant X2 XR_936284.4:n. N/A Genic Downstream Transcript Variant
LOC105372255 transcript variant X4 XR_936285.3: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 GGG= delGG
GRCh38.p14 chr 19 NC_000019.10:g.6138468_6138470= NC_000019.10:g.6138469_6138470del
GRCh37.p13 chr 19 NC_000019.9:g.6138479_6138481= NC_000019.9:g.6138480_6138481del
ACSBG2 transcript variant 1 NM_001289177.2:c.-32+2550= NM_001289177.2:c.-32+2551_-32+2552del
ACSBG2 transcript variant 3 NM_001289178.2:c.-32+2604= NM_001289178.2:c.-32+2605_-32+2606del
ACSBG2 transcript variant 4 NM_001289179.2:c.-32+2559= NM_001289179.2:c.-32+2560_-32+2561del
ACSBG2 transcript variant 5 NM_001289180.2:c.-472+2559= NM_001289180.2:c.-472+2560_-472+2561del
ACSBG2 transcript variant 6 NM_001321384.2:c.-172+2559= NM_001321384.2:c.-172+2560_-172+2561del
ACSBG2 transcript NM_030924.3:c.-32+2559= NM_030924.3:c.-32+2560_-32+2561del
ACSBG2 transcript variant 2 NM_030924.5:c.-32+2559= NM_030924.5:c.-32+2560_-32+2561del
ACSBG2 transcript variant X1 XM_005259649.1:c.-32+2604= XM_005259649.1:c.-32+2605_-32+2606del
ACSBG2 transcript variant X2 XM_005259650.1:c.-32+2550= XM_005259650.1:c.-32+2551_-32+2552del
ACSBG2 transcript variant X4 XM_005259652.1:c.-172+2559= XM_005259652.1:c.-172+2560_-172+2561del
ACSBG2 transcript variant X4 XM_005259653.4:c.-32+2559= XM_005259653.4:c.-32+2560_-32+2561del
ACSBG2 transcript variant X1 XM_017027332.3:c.-32+1053= XM_017027332.3:c.-32+1054_-32+1055del
ACSBG2 transcript variant X2 XM_017027333.2:c.-32+2559= XM_017027333.2:c.-32+2560_-32+2561del
ACSBG2 transcript variant X3 XM_047439477.1:c.-32+2559= XM_047439477.1:c.-32+2560_-32+2561del
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#.

6 SubSNP, 4 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss2960056492 Jan 10, 2018 (151)
2 1000G_HIGH_COVERAGE ss5306360811 Oct 16, 2022 (156)
3 1000G_HIGH_COVERAGE ss5611711755 Oct 16, 2022 (156)
4 TOMMO_GENOMICS ss5784776675 Oct 16, 2022 (156)
5 YY_MCH ss5817372743 Oct 16, 2022 (156)
6 EVA ss5981027554 Oct 16, 2022 (156)
7 1000Genomes_30x NC_000019.10 - 6138468 Oct 16, 2022 (156)
8 gnomAD - Genomes NC_000019.10 - 6138468 Apr 27, 2021 (155)
9 14KJPN NC_000019.10 - 6138468 Oct 16, 2022 (156)
10 ALFA NC_000019.10 - 6138468 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
ss2960056492, ss5981027554 NC_000019.9:6138478:GG: NC_000019.10:6138467:GGG:G (self)
99237690, 533065975, 118613779, ss5306360811, ss5611711755, ss5784776675, ss5817372743 NC_000019.10:6138467:GG: NC_000019.10:6138467:GGG:G (self)
6872877501 NC_000019.10:6138467:GGG:G NC_000019.10:6138467:GGG:G (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 rs1491434709

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