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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.

rs398123072

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:75732682 (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
C>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000032 (8/251342, GnomAD_exome)
T=0.000008 (1/121092, ExAC)
T=0.00006 (2/35910, ALFA) (+ 1 more)
T=0.00030 (5/16760, 8.3KJPN)
Clinical Significance
Reported in ClinVar
Gene : Consequence
ACADM : Missense Variant
Publications
10 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 1 NC_000001.11:g.75732682C>G
GRCh38.p13 chr 1 NC_000001.11:g.75732682C>T
GRCh37.p13 chr 1 NC_000001.10:g.76198367C>G
GRCh37.p13 chr 1 NC_000001.10:g.76198367C>T
ACADM RefSeqGene (LRG_838) NG_007045.2:g.13325C>G
ACADM RefSeqGene (LRG_838) NG_007045.2:g.13325C>T
Gene: ACADM, acyl-CoA dehydrogenase medium chain (plus strand)
Molecule type Change Amino acid[Codon] SO Term
ACADM transcript variant 6 NM_001286044.2:c.-229= N/A 5 Prime UTR Variant
ACADM transcript variant 1 NM_000016.6:c.157C>G R [CGT] > G [GGT] Coding Sequence Variant
medium-chain specific acyl-CoA dehydrogenase, mitochondrial isoform a precursor NP_000007.1:p.Arg53Gly R (Arg) > G (Gly) Missense Variant
ACADM transcript variant 1 NM_000016.6:c.157C>T R [CGT] > C [TGT] Coding Sequence Variant
medium-chain specific acyl-CoA dehydrogenase, mitochondrial isoform a precursor NP_000007.1:p.Arg53Cys R (Arg) > C (Cys) Missense Variant
ACADM transcript variant 5 NM_001286043.2:c.157C>G R [CGT] > G [GGT] Coding Sequence Variant
medium-chain specific acyl-CoA dehydrogenase, mitochondrial isoform d precursor NP_001272972.1:p.Arg53Gly R (Arg) > G (Gly) Missense Variant
ACADM transcript variant 5 NM_001286043.2:c.157C>T R [CGT] > C [TGT] Coding Sequence Variant
medium-chain specific acyl-CoA dehydrogenase, mitochondrial isoform d precursor NP_001272972.1:p.Arg53Cys R (Arg) > C (Cys) Missense Variant
ACADM transcript variant 3 NM_001127328.3:c.169C>G R [CGT] > G [GGT] Coding Sequence Variant
medium-chain specific acyl-CoA dehydrogenase, mitochondrial isoform b precursor NP_001120800.1:p.Arg57Gly R (Arg) > G (Gly) Missense Variant
ACADM transcript variant 3 NM_001127328.3:c.169C>T R [CGT] > C [TGT] Coding Sequence Variant
medium-chain specific acyl-CoA dehydrogenase, mitochondrial isoform b precursor NP_001120800.1:p.Arg57Cys R (Arg) > C (Cys) Missense Variant
ACADM transcript variant 4 NM_001286042.2:c.49C>G R [CGT] > G [GGT] Coding Sequence Variant
medium-chain specific acyl-CoA dehydrogenase, mitochondrial isoform c NP_001272971.1:p.Arg17Gly R (Arg) > G (Gly) Missense Variant
ACADM transcript variant 4 NM_001286042.2:c.49C>T R [CGT] > C [TGT] Coding Sequence Variant
medium-chain specific acyl-CoA dehydrogenase, mitochondrial isoform c NP_001272971.1:p.Arg17Cys R (Arg) > C (Cys) Missense 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: T (allele ID: 98169 )
ClinVar Accession Disease Names Clinical Significance
RCV000077882.6 not provided Pathogenic
RCV000176961.8 Medium-chain acyl-coenzyme A dehydrogenase deficiency 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 35910 C=0.99994 G=0.00000, T=0.00006
European Sub 26588 C=0.99996 G=0.00000, T=0.00004
African Sub 3344 C=1.0000 G=0.0000, T=0.0000
African Others Sub 114 C=1.000 G=0.000, T=0.000
African American Sub 3230 C=1.0000 G=0.0000, T=0.0000
Asian Sub 112 C=1.000 G=0.000, T=0.000
East Asian Sub 86 C=1.00 G=0.00, T=0.00
Other Asian Sub 26 C=1.00 G=0.00, T=0.00
Latin American 1 Sub 500 C=1.000 G=0.000, T=0.000
Latin American 2 Sub 628 C=1.000 G=0.000, T=0.000
South Asian Sub 98 C=1.00 G=0.00, T=0.00
Other Sub 4640 C=0.9998 G=0.0000, T=0.0002


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 - Exomes Global Study-wide 251342 C=0.999968 T=0.000032
gnomAD - Exomes European Sub 135308 C=0.999985 T=0.000015
gnomAD - Exomes Asian Sub 49010 C=0.99990 T=0.00010
gnomAD - Exomes American Sub 34590 C=0.99997 T=0.00003
gnomAD - Exomes African Sub 16224 C=1.00000 T=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10078 C=1.00000 T=0.00000
gnomAD - Exomes Other Sub 6132 C=1.0000 T=0.0000
ExAC Global Study-wide 121092 C=0.999992 T=0.000008
ExAC Europe Sub 73204 C=0.99999 T=0.00001
ExAC Asian Sub 25166 C=1.00000 T=0.00000
ExAC American Sub 11578 C=1.00000 T=0.00000
ExAC African Sub 10236 C=1.00000 T=0.00000
ExAC Other Sub 908 C=1.000 T=0.000
8.3KJPN JAPANESE Study-wide 16760 C=0.99970 T=0.00030
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 C= G T
GRCh38.p13 chr 1 NC_000001.11:g.75732682= NC_000001.11:g.75732682C>G NC_000001.11:g.75732682C>T
GRCh37.p13 chr 1 NC_000001.10:g.76198367= NC_000001.10:g.76198367C>G NC_000001.10:g.76198367C>T
ACADM RefSeqGene (LRG_838) NG_007045.2:g.13325= NG_007045.2:g.13325C>G NG_007045.2:g.13325C>T
ACADM transcript variant 1 NM_000016.6:c.157= NM_000016.6:c.157C>G NM_000016.6:c.157C>T
ACADM transcript variant 1 NM_000016.5:c.157= NM_000016.5:c.157C>G NM_000016.5:c.157C>T
ACADM transcript variant 1 NM_000016.4:c.157= NM_000016.4:c.157C>G NM_000016.4:c.157C>T
ACADM transcript variant 3 NM_001127328.3:c.169= NM_001127328.3:c.169C>G NM_001127328.3:c.169C>T
ACADM transcript variant 3 NM_001127328.2:c.169= NM_001127328.2:c.169C>G NM_001127328.2:c.169C>T
ACADM transcript variant 3 NM_001127328.1:c.169= NM_001127328.1:c.169C>G NM_001127328.1:c.169C>T
ACADM transcript variant 5 NM_001286043.2:c.157= NM_001286043.2:c.157C>G NM_001286043.2:c.157C>T
ACADM transcript variant 5 NM_001286043.1:c.157= NM_001286043.1:c.157C>G NM_001286043.1:c.157C>T
ACADM transcript variant 4 NM_001286042.2:c.49= NM_001286042.2:c.49C>G NM_001286042.2:c.49C>T
ACADM transcript variant 4 NM_001286042.1:c.49= NM_001286042.1:c.49C>G NM_001286042.1:c.49C>T
ACADM transcript variant 6 NM_001286044.2:c.-229= NM_001286044.2:c.-229C>G NM_001286044.2:c.-229C>T
ACADM transcript variant 6 NM_001286044.1:c.-229= NM_001286044.1:c.-229C>G NM_001286044.1:c.-229C>T
ACADM transcript variant 2 NR_022013.1:n.587= NR_022013.1:n.587C>G NR_022013.1:n.587C>T
medium-chain specific acyl-CoA dehydrogenase, mitochondrial isoform a precursor NP_000007.1:p.Arg53= NP_000007.1:p.Arg53Gly NP_000007.1:p.Arg53Cys
medium-chain specific acyl-CoA dehydrogenase, mitochondrial isoform b precursor NP_001120800.1:p.Arg57= NP_001120800.1:p.Arg57Gly NP_001120800.1:p.Arg57Cys
medium-chain specific acyl-CoA dehydrogenase, mitochondrial isoform d precursor NP_001272972.1:p.Arg53= NP_001272972.1:p.Arg53Gly NP_001272972.1:p.Arg53Cys
medium-chain specific acyl-CoA dehydrogenase, mitochondrial isoform c NP_001272971.1:p.Arg17= NP_001272971.1:p.Arg17Gly NP_001272971.1:p.Arg17Cys
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, 8 Frequency, 2 ClinVar submissions
No Submitter Submission ID Date (Build)
1 EGL ss947846724 Jan 23, 2014 (138)
2 EVA_EXAC ss1685603786 Apr 01, 2015 (144)
3 GNOMAD ss2731584853 Nov 08, 2017 (151)
4 ILLUMINA ss3021100352 Nov 08, 2017 (151)
5 TOPMED ss3080387133 Nov 08, 2017 (151)
6 TOPMED ss3080387134 Nov 08, 2017 (151)
7 ILLUMINA ss3651428493 Oct 11, 2018 (152)
8 ILLUMINA ss3725036063 Jul 12, 2019 (153)
9 GNOMAD ss3996152729 Apr 25, 2021 (155)
10 GNOMAD ss3996152730 Apr 25, 2021 (155)
11 TOPMED ss4454846691 Apr 25, 2021 (155)
12 TOPMED ss4454846692 Apr 25, 2021 (155)
13 TOMMO_GENOMICS ss5144582695 Apr 25, 2021 (155)
14 ExAC NC_000001.10 - 76198367 Oct 11, 2018 (152)
15 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 15550975 (NC_000001.11:75732681:C:G 1/140164)
Row 15550976 (NC_000001.11:75732681:C:T 3/140164)

- Apr 25, 2021 (155)
16 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 15550975 (NC_000001.11:75732681:C:G 1/140164)
Row 15550976 (NC_000001.11:75732681:C:T 3/140164)

- Apr 25, 2021 (155)
17 gnomAD - Exomes NC_000001.10 - 76198367 Jul 12, 2019 (153)
18 8.3KJPN NC_000001.10 - 76198367 Apr 25, 2021 (155)
19 TopMed

Submission ignored due to conflicting rows:
Row 18453026 (NC_000001.11:75732681:C:G 1/264690)
Row 18453027 (NC_000001.11:75732681:C:T 3/264690)

- Apr 25, 2021 (155)
20 TopMed

Submission ignored due to conflicting rows:
Row 18453026 (NC_000001.11:75732681:C:G 1/264690)
Row 18453027 (NC_000001.11:75732681:C:T 3/264690)

- Apr 25, 2021 (155)
21 ALFA NC_000001.11 - 75732682 Apr 25, 2021 (155)
22 ClinVar RCV000077882.6 Apr 25, 2020 (154)
23 ClinVar RCV000176961.8 Apr 25, 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
11621913, 13695441994, ss3080387133, ss3996152729, ss4454846691 NC_000001.11:75732681:C:G NC_000001.11:75732681:C:G (self)
4805234, 604777, 2552002, ss1685603786, ss2731584853, ss3021100352, ss3651428493, ss5144582695 NC_000001.10:76198366:C:T NC_000001.11:75732681:C:T (self)
RCV000077882.6, RCV000176961.8, 11621913, 13695441994, ss947846724, ss3080387134, ss3725036063, ss3996152730, ss4454846692 NC_000001.11:75732681:C:T NC_000001.11:75732681:C:T (self)
Help

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

10 citations for rs398123072
PMID Title Author Year Journal
7730333 Effects of two mutations detected in medium chain acyl-CoA dehydrogenase (MCAD)-deficient patients on folding, oligomer assembly, and stability of MCAD enzyme. Bross P et al. 1995 The Journal of biological chemistry
8102510 A rare disease-associated mutation in the medium-chain acyl-CoA dehydrogenase (MCAD) gene changes a conserved arginine, previously shown to be functionally essential in short-chain acyl-CoA dehydrogenase (SCAD). Andresen BS et al. 1993 American journal of human genetics
8535441 Comparison between medium-chain acyl-CoA dehydrogenase mutant proteins overexpressed in bacterial and mammalian cells. Jensen TG et al. 1995 Human mutation
15832312 Population spectrum of ACADM genotypes correlated to biochemical phenotypes in newborn screening for medium-chain acyl-CoA dehydrogenase deficiency. Maier EM et al. 2005 Human mutation
19649258 A novel tandem mass spectrometry method for rapid confirmation of medium- and very long-chain acyl-CoA dehydrogenase deficiency in newborns. ter Veld F et al. 2009 PloS one
20434380 Allelic diversity in MCAD deficiency: the biochemical classification of 54 variants identified during 5 years of ACADM sequencing. Smith EH et al. 2010 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
24623196 Experimental evidence for protein oxidative damage and altered antioxidant defense in patients with medium-chain acyl-CoA dehydrogenase deficiency. Derks TG et al. 2014 Journal of inherited metabolic disease
25741868 Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Richards S et al. 2015 Genetics in medicine
26947917 Significance of ACADM mutations identified through newborn screening of MCAD deficiency in Japan. Hara K et al. 2016 Molecular genetics and metabolism
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