Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

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.

rs387906252

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr17:7222678-7222686 (GRCh38.p13) 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
delAGA
Variation Type
Indel Insertion and Deletion
Frequency
delAGA=0.000019 (5/264690, TOPMED)
delAGA=0.000024 (6/250448, GnomAD_exome)
delAGA=0.000014 (2/140216, GnomAD) (+ 3 more)
delAGA=0.000045 (5/110932, ExAC)
delAGA=0.00024 (4/16760, 8.3KJPN)
delAGA=0.00000 (0/14050, ALFA)
Clinical Significance
Reported in ClinVar
Gene : Consequence
ACADVL : Inframe Deletion
Publications
2 citations
Genomic View
See rs on genome
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.p13 chr 17 NC_000017.11:g.7222678AGA[2]
GRCh37.p13 chr 17 NC_000017.10:g.7125997AGA[2]
DLG4 RefSeqGene NG_008391.2:g.2365TCT[2]
ACADVL RefSeqGene NG_007975.1:g.7845AGA[2]
Gene: ACADVL, acyl-CoA dehydrogenase very long chain (plus strand)
Molecule type Change Amino acid[Codon] SO Term
ACADVL transcript variant 1 NM_000018.4:c.890AGA[2] KK [AAGA] > K [ATG] Coding Sequence Variant
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform 1 precursor NP_000009.1:p.Lys299del KK (LysLys) > K (Lys) Inframe Deletion
ACADVL transcript variant 2 NM_001033859.3:c.824AGA[2] KK [AAGA] > K [ATG] Coding Sequence Variant
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform 2 precursor NP_001029031.1:p.Lys277del KK (LysLys) > K (Lys) Inframe Deletion
ACADVL transcript variant 4 NM_001270448.2:c.662AGA[2] KK [AAGA] > K [ATG] Coding Sequence Variant
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform 4 NP_001257377.1:p.Lys223del KK (LysLys) > K (Lys) Inframe Deletion
ACADVL transcript variant 3 NM_001270447.2:c.959AGA[2] KK [AAGA] > K [ATG] Coding Sequence Variant
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform 3 NP_001257376.1:p.Lys322del KK (LysLys) > K (Lys) Inframe Deletion
ACADVL transcript variant X1 XM_006721516.3:c.890AGA[2] KK [AAGA] > K [ATG] Coding Sequence Variant
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform X1 XP_006721579.2:p.Lys299del KK (LysLys) > K (Lys) Inframe Deletion
ACADVL transcript variant X2 XM_024450741.1:c.890AGA[2] KK [AAGA] > K [ATG] Coding Sequence Variant
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform X2 XP_024306509.1:p.Lys299del KK (LysLys) > K (Lys) Inframe Deletion
ACADVL transcript variant X3 XM_011523829.2:c.890AGA[2] KK [AAGA] > K [ATG] Coding Sequence Variant
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform X3 XP_011522131.1:p.Lys299del KK (LysLys) > K (Lys) Inframe Deletion
ACADVL transcript variant X4 XM_011523830.2:c.890AGA[2] KK [AAGA] > K [ATG] Coding Sequence Variant
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform X4 XP_011522132.1:p.Lys299del KK (LysLys) > K (Lys) Inframe Deletion
ACADVL transcript variant X5 XR_934021.2:n.949AGA[2] N/A Non Coding Transcript Variant
ACADVL transcript variant X6 XR_934022.2:n.949AGA[2] N/A Non Coding Transcript Variant
ACADVL transcript variant X7 XR_934023.2:n.949AGA[2] N/A Non Coding 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.

Allele: delAGA (allele ID: 98203 )
ClinVar Accession Disease Names Clinical Significance
RCV000001694.10 Very long chain acyl-CoA dehydrogenase deficiency Conflicting-Interpretations-Of-Pathogenicity
RCV000077926.6 not provided Pathogenic

ALFA Allele Frequency (New)
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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 14050 AGAAGAAGA=1.00000 AGAAGA=0.00000
European Sub 9690 AGAAGAAGA=1.0000 AGAAGA=0.0000
African Sub 2898 AGAAGAAGA=1.0000 AGAAGA=0.0000
African Others Sub 114 AGAAGAAGA=1.000 AGAAGA=0.000
African American Sub 2784 AGAAGAAGA=1.0000 AGAAGA=0.0000
Asian Sub 112 AGAAGAAGA=1.000 AGAAGA=0.000
East Asian Sub 86 AGAAGAAGA=1.00 AGAAGA=0.00
Other Asian Sub 26 AGAAGAAGA=1.00 AGAAGA=0.00
Latin American 1 Sub 146 AGAAGAAGA=1.000 AGAAGA=0.000
Latin American 2 Sub 610 AGAAGAAGA=1.000 AGAAGA=0.000
South Asian Sub 98 AGAAGAAGA=1.00 AGAAGA=0.00
Other Sub 496 AGAAGAAGA=1.000 AGAAGA=0.000


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
TopMed Global Study-wide 264690 (AGA)3=0.999981 delAGA=0.000019
gnomAD - Exomes Global Study-wide 250448 (AGA)3=0.999976 delAGA=0.000024
gnomAD - Exomes European Sub 134730 (AGA)3=0.999963 delAGA=0.000037
gnomAD - Exomes Asian Sub 48904 (AGA)3=1.00000 delAGA=0.00000
gnomAD - Exomes American Sub 34480 (AGA)3=1.00000 delAGA=0.00000
gnomAD - Exomes African Sub 16174 (AGA)3=0.99994 delAGA=0.00006
gnomAD - Exomes Ashkenazi Jewish Sub 10046 (AGA)3=1.00000 delAGA=0.00000
gnomAD - Exomes Other Sub 6114 (AGA)3=1.0000 delAGA=0.0000
gnomAD - Genomes Global Study-wide 140216 (AGA)3=0.999986 delAGA=0.000014
gnomAD - Genomes European Sub 75930 (AGA)3=1.00000 delAGA=0.00000
gnomAD - Genomes African Sub 42016 (AGA)3=0.99995 delAGA=0.00005
gnomAD - Genomes American Sub 13664 (AGA)3=1.00000 delAGA=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3320 (AGA)3=1.0000 delAGA=0.0000
gnomAD - Genomes East Asian Sub 3134 (AGA)3=1.0000 delAGA=0.0000
gnomAD - Genomes Other Sub 2152 (AGA)3=1.0000 delAGA=0.0000
ExAC Global Study-wide 110932 (AGA)3=0.999955 delAGA=0.000045
ExAC Europe Sub 67270 (AGA)3=0.99994 delAGA=0.00006
ExAC Asian Sub 23098 (AGA)3=1.00000 delAGA=0.00000
ExAC American Sub 10524 (AGA)3=1.00000 delAGA=0.00000
ExAC African Sub 9202 (AGA)3=0.9999 delAGA=0.0001
ExAC Other Sub 838 (AGA)3=1.000 delAGA=0.000
8.3KJPN JAPANESE Study-wide 16760 (AGA)3=0.99976 delAGA=0.00024
Allele Frequency Aggregator Total Global 14050 (AGA)3=1.00000 delAGA=0.00000
Allele Frequency Aggregator European Sub 9690 (AGA)3=1.0000 delAGA=0.0000
Allele Frequency Aggregator African Sub 2898 (AGA)3=1.0000 delAGA=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 (AGA)3=1.000 delAGA=0.000
Allele Frequency Aggregator Other Sub 496 (AGA)3=1.000 delAGA=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 (AGA)3=1.000 delAGA=0.000
Allele Frequency Aggregator Asian Sub 112 (AGA)3=1.000 delAGA=0.000
Allele Frequency Aggregator South Asian Sub 98 (AGA)3=1.00 delAGA=0.00
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 (AGA)3= delAGA
GRCh38.p13 chr 17 NC_000017.11:g.7222678_7222686= NC_000017.11:g.7222678AGA[2]
GRCh37.p13 chr 17 NC_000017.10:g.7125997_7126005= NC_000017.10:g.7125997AGA[2]
DLG4 RefSeqGene NG_008391.2:g.2365_2373= NG_008391.2:g.2365TCT[2]
ACADVL RefSeqGene NG_007975.1:g.7845_7853= NG_007975.1:g.7845AGA[2]
ACADVL transcript variant 1 NM_000018.4:c.890_898= NM_000018.4:c.890AGA[2]
ACADVL transcript variant 1 NM_000018.3:c.890_898= NM_000018.3:c.890AGA[2]
ACADVL transcript variant 2 NM_001033859.3:c.824_832= NM_001033859.3:c.824AGA[2]
ACADVL transcript variant 2 NM_001033859.2:c.824_832= NM_001033859.2:c.824AGA[2]
ACADVL transcript variant 4 NM_001270448.2:c.662_670= NM_001270448.2:c.662AGA[2]
ACADVL transcript variant 4 NM_001270448.1:c.662_670= NM_001270448.1:c.662AGA[2]
ACADVL transcript variant 3 NM_001270447.2:c.959_967= NM_001270447.2:c.959AGA[2]
ACADVL transcript variant 3 NM_001270447.1:c.959_967= NM_001270447.1:c.959AGA[2]
ACADVL transcript variant X1 XM_006721516.3:c.890_898= XM_006721516.3:c.890AGA[2]
ACADVL transcript variant X5 XR_934021.2:n.949_957= XR_934021.2:n.949AGA[2]
ACADVL transcript variant X7 XR_934023.2:n.949_957= XR_934023.2:n.949AGA[2]
ACADVL transcript variant X3 XM_011523829.2:c.890_898= XM_011523829.2:c.890AGA[2]
ACADVL transcript variant X6 XR_934022.2:n.949_957= XR_934022.2:n.949AGA[2]
ACADVL transcript variant X4 XM_011523830.2:c.890_898= XM_011523830.2:c.890AGA[2]
ACADVL transcript variant X2 XM_024450741.1:c.890_898= XM_024450741.1:c.890AGA[2]
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform 1 precursor NP_000009.1:p.Glu297_Met300= NP_000009.1:p.Lys299del
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform 2 precursor NP_001029031.1:p.Glu275_Met278= NP_001029031.1:p.Lys277del
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform 4 NP_001257377.1:p.Glu221_Met224= NP_001257377.1:p.Lys223del
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform 3 NP_001257376.1:p.Glu320_Met323= NP_001257376.1:p.Lys322del
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform X1 XP_006721579.2:p.Glu297_Met300= XP_006721579.2:p.Lys299del
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform X3 XP_011522131.1:p.Glu297_Met300= XP_011522131.1:p.Lys299del
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform X4 XP_011522132.1:p.Glu297_Met300= XP_011522132.1:p.Lys299del
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform X2 XP_024306509.1:p.Glu297_Met300= XP_024306509.1:p.Lys299del
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#.

13 SubSNP, 6 Frequency, 2 ClinVar submissions
No Submitter Submission ID Date (Build)
1 OMIM-CURATED-RECORDS ss825076766 Jun 20, 2013 (137)
2 EGL ss947846752 Jan 23, 2014 (136)
3 EVA_EXAC ss1712128592 Apr 01, 2015 (136)
4 TOPMED ss2380138990 Dec 20, 2016 (136)
5 GNOMAD ss2742385785 Nov 08, 2017 (151)
6 GNOMAD ss2749672703 Nov 08, 2017 (151)
7 GNOMAD ss2947395513 Nov 08, 2017 (151)
8 ILLUMINA ss3021751289 Nov 08, 2017 (151)
9 TOPMED ss3256594385 Nov 08, 2017 (151)
10 ILLUMINA ss3652164068 Oct 12, 2018 (152)
11 ILLUMINA ss3725599186 Jul 13, 2019 (153)
12 TOPMED ss5028550619 Apr 27, 2021 (155)
13 TOMMO_GENOMICS ss5221371740 Apr 27, 2021 (155)
14 ExAC NC_000017.10 - 7125997 Oct 12, 2018 (152)
15 gnomAD - Genomes NC_000017.11 - 7222678 Apr 27, 2021 (155)
16 gnomAD - Exomes NC_000017.10 - 7125997 Jul 13, 2019 (153)
17 8.3KJPN NC_000017.10 - 7125997 Apr 27, 2021 (155)
18 TopMed NC_000017.11 - 7222678 Apr 27, 2021 (155)
19 ALFA NC_000017.11 - 7222678 Apr 27, 2021 (155)
20 ClinVar RCV000001694.10 Apr 27, 2021 (155)
21 ClinVar RCV000077926.6 Apr 27, 2020 (154)
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).

Associated ID History Updated (Build)
rs398123094 May 11, 2017 (136)
rs761162357 Feb 27, 2017 (136)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
2990299, 11683237, 79341047, ss1712128592, ss2380138990, ss2742385785, ss2749672703, ss2947395513, ss3021751289, ss3652164068, ss5221371740 NC_000017.10:7125996:AGA: NC_000017.11:7222677:AGAAGAAGA:AGA…

NC_000017.11:7222677:AGAAGAAGA:AGAAGA

(self)
500716224, 152330588, 244096281, ss3256594385, ss3725599186, ss5028550619 NC_000017.11:7222677:AGA: NC_000017.11:7222677:AGAAGAAGA:AGA…

NC_000017.11:7222677:AGAAGAAGA:AGAAGA

(self)
RCV000001694.10, RCV000077926.6, 1697543626 NC_000017.11:7222677:AGAAGAAGA:AGA…

NC_000017.11:7222677:AGAAGAAGA:AGAAGA

NC_000017.11:7222677:AGAAGAAGA:AGA…

NC_000017.11:7222677:AGAAGAAGA:AGAAGA

(self)
ss825076766 NC_000017.11:7222682:AAG: NC_000017.11:7222677:AGAAGAAGA:AGA…

NC_000017.11:7222677:AGAAGAAGA:AGAAGA

(self)
ss947846752 NC_000017.11:7222683:AGA: NC_000017.11:7222677:AGAAGAAGA:AGA…

NC_000017.11:7222677:AGAAGAAGA:AGAAGA

(self)
Help

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

2 citations for rs387906252
PMID Title Author Year Journal
8554073 Mutation analysis of very-long-chain acyl-coenzyme A dehydrogenase (VLCAD) deficiency: identification and characterization of mutant VLCAD cDNAs from four patients. Souri M et al. 1996 American journal of human genetics
23757202 Free the data: one laboratory's approach to knowledge-based genomic variant classification and preparation for EMR integration of genomic data. Bean LJ et al. 2013 Human mutation
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.post596+ae089ad