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.

rs398123090

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr17:7221665 (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
T>A / T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.000004 (1/264690, TOPMED)
C=0.000004 (1/251270, GnomAD_exome)
C=0.000007 (1/140142, GnomAD) (+ 2 more)
C=0.000008 (1/120648, ExAC)
C=0.00000 (0/14526, ALFA)
Clinical Significance
Reported in ClinVar
Gene : Consequence
ACADVL : Missense Variant
DLG4 : 2KB Upstream Variant
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.7221665T>A
GRCh38.p13 chr 17 NC_000017.11:g.7221665T>C
GRCh37.p13 chr 17 NC_000017.10:g.7124984T>A
GRCh37.p13 chr 17 NC_000017.10:g.7124984T>C
DLG4 RefSeqGene NG_008391.2:g.3386A>T
DLG4 RefSeqGene NG_008391.2:g.3386A>G
ACADVL RefSeqGene NG_007975.1:g.6832T>A
ACADVL RefSeqGene NG_007975.1:g.6832T>C
Gene: DLG4, discs large MAGUK scaffold protein 4 (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
DLG4 transcript variant 3 NM_001321074.1:c. N/A Upstream Transcript Variant
DLG4 transcript variant 1 NM_001365.4:c. N/A Upstream Transcript Variant
DLG4 transcript variant 2 NM_001128827.4:c. N/A N/A
DLG4 transcript variant 4 NM_001321075.3:c. N/A N/A
DLG4 transcript variant 5 NM_001321076.3:c. N/A N/A
DLG4 transcript variant 6 NM_001321077.3:c. N/A N/A
DLG4 transcript variant 8 NM_001369566.3:c. N/A N/A
DLG4 transcript variant 7 NR_135527.1:n. N/A Upstream Transcript Variant
DLG4 transcript variant X1 XM_011523699.2:c. N/A Upstream Transcript Variant
DLG4 transcript variant X2 XM_005256491.1:c. N/A N/A
DLG4 transcript variant X8 XM_011523702.1:c. N/A N/A
DLG4 transcript variant X4 XM_017024288.2:c. N/A N/A
DLG4 transcript variant X5 XM_017024289.2:c. N/A N/A
DLG4 transcript variant X3 XM_024450629.1:c. N/A N/A
DLG4 transcript variant X7 XR_934005.2:n. N/A Upstream Transcript Variant
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.605T>A L [CTC] > H [CAC] Coding Sequence Variant
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform 1 precursor NP_000009.1:p.Leu202His L (Leu) > H (His) Missense Variant
ACADVL transcript variant 1 NM_000018.4:c.605T>C L [CTC] > P [CCC] Coding Sequence Variant
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform 1 precursor NP_000009.1:p.Leu202Pro L (Leu) > P (Pro) Missense Variant
ACADVL transcript variant 2 NM_001033859.3:c.539T>A L [CTC] > H [CAC] Coding Sequence Variant
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform 2 precursor NP_001029031.1:p.Leu180His L (Leu) > H (His) Missense Variant
ACADVL transcript variant 2 NM_001033859.3:c.539T>C L [CTC] > P [CCC] Coding Sequence Variant
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform 2 precursor NP_001029031.1:p.Leu180Pro L (Leu) > P (Pro) Missense Variant
ACADVL transcript variant 4 NM_001270448.2:c.377T>A L [CTC] > H [CAC] Coding Sequence Variant
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform 4 NP_001257377.1:p.Leu126His L (Leu) > H (His) Missense Variant
ACADVL transcript variant 4 NM_001270448.2:c.377T>C L [CTC] > P [CCC] Coding Sequence Variant
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform 4 NP_001257377.1:p.Leu126Pro L (Leu) > P (Pro) Missense Variant
ACADVL transcript variant 3 NM_001270447.2:c.674T>A L [CTC] > H [CAC] Coding Sequence Variant
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform 3 NP_001257376.1:p.Leu225His L (Leu) > H (His) Missense Variant
ACADVL transcript variant 3 NM_001270447.2:c.674T>C L [CTC] > P [CCC] Coding Sequence Variant
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform 3 NP_001257376.1:p.Leu225Pro L (Leu) > P (Pro) Missense Variant
ACADVL transcript variant X1 XM_006721516.3:c.605T>A L [CTC] > H [CAC] Coding Sequence Variant
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform X1 XP_006721579.2:p.Leu202His L (Leu) > H (His) Missense Variant
ACADVL transcript variant X1 XM_006721516.3:c.605T>C L [CTC] > P [CCC] Coding Sequence Variant
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform X1 XP_006721579.2:p.Leu202Pro L (Leu) > P (Pro) Missense Variant
ACADVL transcript variant X2 XM_024450741.1:c.605T>A L [CTC] > H [CAC] Coding Sequence Variant
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform X2 XP_024306509.1:p.Leu202His L (Leu) > H (His) Missense Variant
ACADVL transcript variant X2 XM_024450741.1:c.605T>C L [CTC] > P [CCC] Coding Sequence Variant
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform X2 XP_024306509.1:p.Leu202Pro L (Leu) > P (Pro) Missense Variant
ACADVL transcript variant X3 XM_011523829.2:c.605T>A L [CTC] > H [CAC] Coding Sequence Variant
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform X3 XP_011522131.1:p.Leu202His L (Leu) > H (His) Missense Variant
ACADVL transcript variant X3 XM_011523829.2:c.605T>C L [CTC] > P [CCC] Coding Sequence Variant
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform X3 XP_011522131.1:p.Leu202Pro L (Leu) > P (Pro) Missense Variant
ACADVL transcript variant X4 XM_011523830.2:c.605T>A L [CTC] > H [CAC] Coding Sequence Variant
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform X4 XP_011522132.1:p.Leu202His L (Leu) > H (His) Missense Variant
ACADVL transcript variant X4 XM_011523830.2:c.605T>C L [CTC] > P [CCC] Coding Sequence Variant
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform X4 XP_011522132.1:p.Leu202Pro L (Leu) > P (Pro) Missense Variant
ACADVL transcript variant X5 XR_934021.2:n.664T>A N/A Non Coding Transcript Variant
ACADVL transcript variant X5 XR_934021.2:n.664T>C N/A Non Coding Transcript Variant
ACADVL transcript variant X6 XR_934022.2:n.664T>A N/A Non Coding Transcript Variant
ACADVL transcript variant X6 XR_934022.2:n.664T>C N/A Non Coding Transcript Variant
ACADVL transcript variant X7 XR_934023.2:n.664T>A N/A Non Coding Transcript Variant
ACADVL transcript variant X7 XR_934023.2:n.664T>C 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: A (allele ID: 98198 )
ClinVar Accession Disease Names Clinical Significance
RCV000077920.4 not provided Uncertain-Significance
RCV001001444.2 Very long chain acyl-CoA dehydrogenase deficiency Uncertain-Significance
Allele: C (allele ID: 98199 )
ClinVar Accession Disease Names Clinical Significance
RCV000723640.2 not provided Uncertain-Significance
RCV001200734.2 Very long chain acyl-CoA dehydrogenase deficiency Conflicting-Interpretations-Of-Pathogenicity

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 14526 T=1.00000 C=0.00000
European Sub 9690 T=1.0000 C=0.0000
African Sub 3322 T=1.0000 C=0.0000
African Others Sub 114 T=1.000 C=0.000
African American Sub 3208 T=1.0000 C=0.0000
Asian Sub 112 T=1.000 C=0.000
East Asian Sub 86 T=1.00 C=0.00
Other Asian Sub 26 T=1.00 C=0.00
Latin American 1 Sub 146 T=1.000 C=0.000
Latin American 2 Sub 610 T=1.000 C=0.000
South Asian Sub 98 T=1.00 C=0.00
Other Sub 548 T=1.000 C=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 T=0.999996 C=0.000004
gnomAD - Exomes Global Study-wide 251270 T=0.999996 C=0.000004
gnomAD - Exomes European Sub 135246 T=1.000000 C=0.000000
gnomAD - Exomes Asian Sub 49004 T=1.00000 C=0.00000
gnomAD - Exomes American Sub 34584 T=1.00000 C=0.00000
gnomAD - Exomes African Sub 16230 T=1.00000 C=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10074 T=1.00000 C=0.00000
gnomAD - Exomes Other Sub 6132 T=0.9998 C=0.0002
gnomAD - Genomes Global Study-wide 140142 T=0.999993 C=0.000007
gnomAD - Genomes European Sub 75936 T=0.99999 C=0.00001
gnomAD - Genomes African Sub 41974 T=1.00000 C=0.00000
gnomAD - Genomes American Sub 13642 T=1.00000 C=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3320 T=1.0000 C=0.0000
gnomAD - Genomes East Asian Sub 3132 T=1.0000 C=0.0000
gnomAD - Genomes Other Sub 2138 T=1.0000 C=0.0000
ExAC Global Study-wide 120648 T=0.999992 C=0.000008
ExAC Europe Sub 72798 T=0.99999 C=0.00001
ExAC Asian Sub 25152 T=1.00000 C=0.00000
ExAC American Sub 11562 T=1.00000 C=0.00000
ExAC African Sub 10240 T=1.00000 C=0.00000
ExAC Other Sub 896 T=1.000 C=0.000
Allele Frequency Aggregator Total Global 14526 T=1.00000 C=0.00000
Allele Frequency Aggregator European Sub 9690 T=1.0000 C=0.0000
Allele Frequency Aggregator African Sub 3322 T=1.0000 C=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 T=1.000 C=0.000
Allele Frequency Aggregator Other Sub 548 T=1.000 C=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 T=1.000 C=0.000
Allele Frequency Aggregator Asian Sub 112 T=1.000 C=0.000
Allele Frequency Aggregator South Asian Sub 98 T=1.00 C=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 T= A C
GRCh38.p13 chr 17 NC_000017.11:g.7221665= NC_000017.11:g.7221665T>A NC_000017.11:g.7221665T>C
GRCh37.p13 chr 17 NC_000017.10:g.7124984= NC_000017.10:g.7124984T>A NC_000017.10:g.7124984T>C
DLG4 RefSeqGene NG_008391.2:g.3386= NG_008391.2:g.3386A>T NG_008391.2:g.3386A>G
ACADVL RefSeqGene NG_007975.1:g.6832= NG_007975.1:g.6832T>A NG_007975.1:g.6832T>C
ACADVL transcript variant 1 NM_000018.4:c.605= NM_000018.4:c.605T>A NM_000018.4:c.605T>C
ACADVL transcript variant 1 NM_000018.3:c.605= NM_000018.3:c.605T>A NM_000018.3:c.605T>C
ACADVL transcript variant 2 NM_001033859.3:c.539= NM_001033859.3:c.539T>A NM_001033859.3:c.539T>C
ACADVL transcript variant 2 NM_001033859.2:c.539= NM_001033859.2:c.539T>A NM_001033859.2:c.539T>C
ACADVL transcript variant 4 NM_001270448.2:c.377= NM_001270448.2:c.377T>A NM_001270448.2:c.377T>C
ACADVL transcript variant 4 NM_001270448.1:c.377= NM_001270448.1:c.377T>A NM_001270448.1:c.377T>C
ACADVL transcript variant 3 NM_001270447.2:c.674= NM_001270447.2:c.674T>A NM_001270447.2:c.674T>C
ACADVL transcript variant 3 NM_001270447.1:c.674= NM_001270447.1:c.674T>A NM_001270447.1:c.674T>C
ACADVL transcript variant X1 XM_006721516.3:c.605= XM_006721516.3:c.605T>A XM_006721516.3:c.605T>C
ACADVL transcript variant X5 XR_934021.2:n.664= XR_934021.2:n.664T>A XR_934021.2:n.664T>C
ACADVL transcript variant X7 XR_934023.2:n.664= XR_934023.2:n.664T>A XR_934023.2:n.664T>C
ACADVL transcript variant X3 XM_011523829.2:c.605= XM_011523829.2:c.605T>A XM_011523829.2:c.605T>C
ACADVL transcript variant X6 XR_934022.2:n.664= XR_934022.2:n.664T>A XR_934022.2:n.664T>C
ACADVL transcript variant X4 XM_011523830.2:c.605= XM_011523830.2:c.605T>A XM_011523830.2:c.605T>C
ACADVL transcript variant X2 XM_024450741.1:c.605= XM_024450741.1:c.605T>A XM_024450741.1:c.605T>C
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform 1 precursor NP_000009.1:p.Leu202= NP_000009.1:p.Leu202His NP_000009.1:p.Leu202Pro
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform 2 precursor NP_001029031.1:p.Leu180= NP_001029031.1:p.Leu180His NP_001029031.1:p.Leu180Pro
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform 4 NP_001257377.1:p.Leu126= NP_001257377.1:p.Leu126His NP_001257377.1:p.Leu126Pro
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform 3 NP_001257376.1:p.Leu225= NP_001257376.1:p.Leu225His NP_001257376.1:p.Leu225Pro
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform X1 XP_006721579.2:p.Leu202= XP_006721579.2:p.Leu202His XP_006721579.2:p.Leu202Pro
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform X3 XP_011522131.1:p.Leu202= XP_011522131.1:p.Leu202His XP_011522131.1:p.Leu202Pro
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform X4 XP_011522132.1:p.Leu202= XP_011522132.1:p.Leu202His XP_011522132.1:p.Leu202Pro
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform X2 XP_024306509.1:p.Leu202= XP_024306509.1:p.Leu202His XP_024306509.1:p.Leu202Pro
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#.

10 SubSNP, 5 Frequency, 4 ClinVar submissions
No Submitter Submission ID Date (Build)
1 EGL ss947846747 Jan 23, 2014 (138)
2 EGL ss947846748 Jan 23, 2014 (138)
3 EVA_EXAC ss1692563605 Apr 01, 2015 (144)
4 GNOMAD ss2742385613 Nov 08, 2017 (151)
5 ILLUMINA ss3021751267 Nov 08, 2017 (151)
6 TOPMED ss3256594162 Nov 08, 2017 (151)
7 ILLUMINA ss3652164046 Oct 12, 2018 (152)
8 ILLUMINA ss3725599167 Jul 13, 2019 (153)
9 GNOMAD ss4307501921 Apr 27, 2021 (155)
10 TOPMED ss5028550297 Apr 27, 2021 (155)
11 ExAC NC_000017.10 - 7124984 Oct 12, 2018 (152)
12 gnomAD - Genomes NC_000017.11 - 7221665 Apr 27, 2021 (155)
13 gnomAD - Exomes NC_000017.10 - 7124984 Jul 13, 2019 (153)
14 TopMed NC_000017.11 - 7221665 Apr 27, 2021 (155)
15 ALFA NC_000017.11 - 7221665 Apr 27, 2021 (155)
16 ClinVar RCV000077920.4 Oct 12, 2018 (152)
17 ClinVar RCV000723640.2 Jul 13, 2019 (153)
18 ClinVar RCV001001444.2 Apr 27, 2021 (155)
19 ClinVar RCV001200734.2 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
RCV000077920.4, RCV001001444.2, ss947846747 NC_000017.11:7221664:T:A NC_000017.11:7221664:T:A (self)
2990153, 11683033, ss1692563605, ss2742385613, ss3021751267, ss3652164046 NC_000017.10:7124983:T:C NC_000017.11:7221664:T:C (self)
RCV000723640.2, RCV001200734.2, 500715974, 152330383, 244095959, 841304116, ss947846748, ss3256594162, ss3725599167, ss4307501921, ss5028550297 NC_000017.11:7221664:T:C NC_000017.11:7221664:T:C (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 rs398123090
PMID Title Author Year Journal
23480858 Molecular and cellular pathology of very-long-chain acyl-CoA dehydrogenase deficiency. Schiff M et al. 2013 Molecular genetics and metabolism
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