Name: rs398123085
Published: September 21, 2022
License: Open Access

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.

rs398123085

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr17:7224674 (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: G>A / G>C
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.000004 (1/264690, TOPMED)
A=0.000027 (5/188114, GnomAD_exome)
A=0.00009 (4/43944, ALFA) (+ 1 more)
A=0.00003 (1/29950, ExAC)

Clinical Significance: Reported in ClinVar
Gene : Consequence: ACADVL : Missense Variant
MIR324 : 2KB Upstream Variant
Publications: 1 citation
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: 20230706150541

Population	Group	Sample Size	Ref Allele	Alt Allele
Total	Global	43944	G=0.99991	A=0.00009, C=0.00000
European	Sub	32320	G=0.99991	A=0.00009, C=0.00000
African	Sub	3512	G=1.0000	A=0.0000, C=0.0000
African Others	Sub	122	G=1.000	A=0.000, C=0.000
African American	Sub	3390	G=1.0000	A=0.0000, C=0.0000
Asian	Sub	168	G=1.000	A=0.000, C=0.000
East Asian	Sub	112	G=1.000	A=0.000, C=0.000
Other Asian	Sub	56	G=1.00	A=0.00, C=0.00
Latin American 1	Sub	464	G=1.000	A=0.000, C=0.000
Latin American 2	Sub	628	G=1.000	A=0.000, C=0.000
South Asian	Sub	98	G=1.00	A=0.00, C=0.00
Other	Sub	6754	G=0.9999	A=0.0001, C=0.0000

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").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	G=0.999996	C=0.000004
gnomAD - Exomes	Global	Study-wide	188114	G=0.999973	A=0.000027
gnomAD - Exomes	European	Sub	95784	G=0.99995	A=0.00005
gnomAD - Exomes	Asian	Sub	39646	G=1.00000	A=0.00000
gnomAD - Exomes	American	Sub	27750	G=1.00000	A=0.00000
gnomAD - Exomes	African	Sub	11092	G=1.00000	A=0.00000
gnomAD - Exomes	Ashkenazi Jewish	Sub	8874	G=1.0000	A=0.0000
gnomAD - Exomes	Other	Sub	4968	G=1.0000	A=0.0000
Allele Frequency Aggregator	Total	Global	43944	G=0.99991	A=0.00009, C=0.00000
Allele Frequency Aggregator	European	Sub	32320	G=0.99991	A=0.00009, C=0.00000
Allele Frequency Aggregator	Other	Sub	6754	G=0.9999	A=0.0001, C=0.0000
Allele Frequency Aggregator	African	Sub	3512	G=1.0000	A=0.0000, C=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	628	G=1.000	A=0.000, C=0.000
Allele Frequency Aggregator	Latin American 1	Sub	464	G=1.000	A=0.000, C=0.000
Allele Frequency Aggregator	Asian	Sub	168	G=1.000	A=0.000, C=0.000
Allele Frequency Aggregator	South Asian	Sub	98	G=1.00	A=0.00, C=0.00
ExAC	Global	Study-wide	29950	G=0.99997	A=0.00003
ExAC	Europe	Sub	14420	G=0.99993	A=0.00007
ExAC	Asian	Sub	10608	G=1.00000	A=0.00000
ExAC	African	Sub	3378	G=1.0000	A=0.0000
ExAC	American	Sub	1294	G=1.0000	A=0.0000
ExAC	Other	Sub	250	G=1.000	A=0.000

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.7224674G>A
GRCh38.p14 chr 17	NC_000017.11:g.7224674G>C
GRCh37.p13 chr 17	NC_000017.10:g.7127993G>A
GRCh37.p13 chr 17	NC_000017.10:g.7127993G>C
DLG4 RefSeqGene	NG_008391.2:g.377C>T
DLG4 RefSeqGene	NG_008391.2:g.377C>G
DVL2 RefSeqGene	NG_033038.1:g.14871C>T
DVL2 RefSeqGene	NG_033038.1:g.14871C>G
ACADVL RefSeqGene	NG_007975.1:g.9841G>A
ACADVL RefSeqGene	NG_007975.1:g.9841G>C

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.1711G>A	G [GGG] > R [AGG]	Coding Sequence Variant
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform 1 precursor	NP_000009.1:p.Gly571Arg	G (Gly) > R (Arg)	Missense Variant
ACADVL transcript variant 1	NM_000018.4:c.1711G>C	G [GGG] > R [CGG]	Coding Sequence Variant
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform 1 precursor	NP_000009.1:p.Gly571Arg	G (Gly) > R (Arg)	Missense Variant
ACADVL transcript variant 2	NM_001033859.3:c.1645G>A	G [GGG] > R [AGG]	Coding Sequence Variant
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform 2 precursor	NP_001029031.1:p.Gly549Arg	G (Gly) > R (Arg)	Missense Variant
ACADVL transcript variant 2	NM_001033859.3:c.1645G>C	G [GGG] > R [CGG]	Coding Sequence Variant
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform 2 precursor	NP_001029031.1:p.Gly549Arg	G (Gly) > R (Arg)	Missense Variant
ACADVL transcript variant 4	NM_001270448.2:c.1483G>A	G [GGG] > R [AGG]	Coding Sequence Variant
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform 4	NP_001257377.1:p.Gly495Arg	G (Gly) > R (Arg)	Missense Variant
ACADVL transcript variant 4	NM_001270448.2:c.1483G>C	G [GGG] > R [CGG]	Coding Sequence Variant
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform 4	NP_001257377.1:p.Gly495Arg	G (Gly) > R (Arg)	Missense Variant
ACADVL transcript variant 3	NM_001270447.2:c.1780G>A	G [GGG] > R [AGG]	Coding Sequence Variant
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform 3	NP_001257376.1:p.Gly594Arg	G (Gly) > R (Arg)	Missense Variant
ACADVL transcript variant 3	NM_001270447.2:c.1780G>C	G [GGG] > R [CGG]	Coding Sequence Variant
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform 3	NP_001257376.1:p.Gly594Arg	G (Gly) > R (Arg)	Missense Variant
ACADVL transcript variant X1	XM_006721516.4:c.1679-41G… XM_006721516.4:c.1679-41G>A	N/A	Intron Variant
ACADVL transcript variant X2	XM_011523829.3:c.1577-41G… XM_011523829.3:c.1577-41G>A	N/A	Intron Variant
ACADVL transcript variant X6	XM_047435932.1:c.1581-41G… XM_047435932.1:c.1581-41G>A	N/A	Intron Variant
ACADVL transcript variant X4	XM_047435931.1:c.	N/A	Genic Downstream Transcript Variant
ACADVL transcript variant X3	XM_011523830.3:c.1609G>A	G [GGG] > R [AGG]	Coding Sequence Variant
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform X3	XP_011522132.1:p.Gly537Arg	G (Gly) > R (Arg)	Missense Variant
ACADVL transcript variant X3	XM_011523830.3:c.1609G>C	G [GGG] > R [CGG]	Coding Sequence Variant
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform X3	XP_011522132.1:p.Gly537Arg	G (Gly) > R (Arg)	Missense Variant
ACADVL transcript variant X5	XR_007065296.1:n.1660G>A	N/A	Non Coding Transcript Variant
ACADVL transcript variant X5	XR_007065296.1:n.1660G>C	N/A	Non Coding Transcript Variant

Gene: MIR324, microRNA 324 (minus strand) : 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
MIR324 transcript	NR_029896.1:n.	N/A	Upstream Transcript Variant

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: 98190 )

ClinVar Accession	Disease Names	Clinical Significance
RCV000077910.8	not provided	Uncertain-Significance
RCV001200766.5	Very long chain acyl-CoA dehydrogenase deficiency	Uncertain-Significance

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	G=	A	C
GRCh38.p14 chr 17	NC_000017.11:g.7224674=	NC_000017.11:g.7224674G>A	NC_000017.11:g.7224674G>C
GRCh37.p13 chr 17	NC_000017.10:g.7127993=	NC_000017.10:g.7127993G>A	NC_000017.10:g.7127993G>C
DLG4 RefSeqGene	NG_008391.2:g.377=	NG_008391.2:g.377C>T	NG_008391.2:g.377C>G
DVL2 RefSeqGene	NG_033038.1:g.14871=	NG_033038.1:g.14871C>T	NG_033038.1:g.14871C>G
ACADVL RefSeqGene	NG_007975.1:g.9841=	NG_007975.1:g.9841G>A	NG_007975.1:g.9841G>C
ACADVL transcript variant 1	NM_000018.4:c.1711=	NM_000018.4:c.1711G>A	NM_000018.4:c.1711G>C
ACADVL transcript variant 1	NM_000018.3:c.1711=	NM_000018.3:c.1711G>A	NM_000018.3:c.1711G>C
ACADVL transcript variant 2	NM_001033859.3:c.1645=	NM_001033859.3:c.1645G>A	NM_001033859.3:c.1645G>C
ACADVL transcript variant 2	NM_001033859.2:c.1645=	NM_001033859.2:c.1645G>A	NM_001033859.2:c.1645G>C
ACADVL transcript variant 4	NM_001270448.2:c.1483=	NM_001270448.2:c.1483G>A	NM_001270448.2:c.1483G>C
ACADVL transcript variant 4	NM_001270448.1:c.1483=	NM_001270448.1:c.1483G>A	NM_001270448.1:c.1483G>C
ACADVL transcript variant 3	NM_001270447.2:c.1780=	NM_001270447.2:c.1780G>A	NM_001270447.2:c.1780G>C
ACADVL transcript variant 3	NM_001270447.1:c.1780=	NM_001270447.1:c.1780G>A	NM_001270447.1:c.1780G>C
ACADVL transcript variant X3	XM_011523830.3:c.1609=	XM_011523830.3:c.1609G>A	XM_011523830.3:c.1609G>C
ACADVL transcript variant X4	XM_011523830.2:c.1609=	XM_011523830.2:c.1609G>A	XM_011523830.2:c.1609G>C
ACADVL transcript variant X3	XM_011523830.1:c.1609=	XM_011523830.1:c.1609G>A	XM_011523830.1:c.1609G>C
ACADVL transcript variant X5	XR_007065296.1:n.1660=	XR_007065296.1:n.1660G>A	XR_007065296.1:n.1660G>C
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform 1 precursor	NP_000009.1:p.Gly571=	NP_000009.1:p.Gly571Arg	NP_000009.1:p.Gly571Arg
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform 2 precursor	NP_001029031.1:p.Gly549=	NP_001029031.1:p.Gly549Arg	NP_001029031.1:p.Gly549Arg
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform 4	NP_001257377.1:p.Gly495=	NP_001257377.1:p.Gly495Arg	NP_001257377.1:p.Gly495Arg
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform 3	NP_001257376.1:p.Gly594=	NP_001257376.1:p.Gly594Arg	NP_001257376.1:p.Gly594Arg
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform X3	XP_011522132.1:p.Gly537=	XP_011522132.1:p.Gly537Arg	XP_011522132.1:p.Gly537Arg
ACADVL transcript variant X1	XM_006721516.4:c.1679-41=	XM_006721516.4:c.1679-41G>A	XM_006721516.4:c.1679-41G>C
ACADVL transcript variant X2	XM_011523829.3:c.1577-41=	XM_011523829.3:c.1577-41G>A	XM_011523829.3:c.1577-41G>C
ACADVL transcript variant X6	XM_047435932.1:c.1581-41=	XM_047435932.1:c.1581-41G>A	XM_047435932.1:c.1581-41G>C

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, 6 Frequency, 2 ClinVar submissions

No	Submitter	Submission ID	Date (Build)
1	EGL	ss947846739	Jan 23, 2014 (138)
2	EVA_EXAC	ss1692564075	Apr 01, 2015 (144)
3	GNOMAD	ss2742386269	Nov 08, 2017 (151)
4	GNOMAD	ss4307502334	Apr 27, 2021 (155)
5	GNOMAD	ss4307502335	Apr 27, 2021 (155)
6	TOPMED	ss5028551141	Apr 27, 2021 (155)
7	ExAC	NC_000017.10 - 7127993	Oct 12, 2018 (152)
8	gnomAD - Genomes Submission ignored due to conflicting rows: Row 500716643 (NC_000017.11:7224673:G:A 5/132138) Row 500716644 (NC_000017.11:7224673:G:C 1/132138)	-	Apr 27, 2021 (155)
9	gnomAD - Genomes Submission ignored due to conflicting rows: Row 500716643 (NC_000017.11:7224673:G:A 5/132138) Row 500716644 (NC_000017.11:7224673:G:C 1/132138)	-	Apr 27, 2021 (155)
10	gnomAD - Exomes	NC_000017.10 - 7127993	Jul 13, 2019 (153)
11	TopMed	NC_000017.11 - 7224674	Apr 27, 2021 (155)
12	ALFA	NC_000017.11 - 7224674	Apr 27, 2021 (155)
13	ClinVar	RCV000077910.8	Oct 16, 2022 (156)
14	ClinVar	RCV001200766.5	Oct 16, 2022 (156)

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
2990663, 11683791, ss1692564075, ss2742386269	NC_000017.10:7127992:G:A	NC_000017.11:7224673:G:A	(self)
RCV000077910.8, RCV001200766.5, 7578513416, ss947846739, ss4307502334	NC_000017.11:7224673:G:A	NC_000017.11:7224673:G:A	(self)
244096803, 7578513416, ss4307502335, ss5028551141	NC_000017.11:7224673:G:C	NC_000017.11:7224673:G:C	(self)

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

1 citation for rs398123085

PMID	Title	Author	Year	Journal
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

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs398123085