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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.

rs398123077

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:75734878 (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
A>G / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.000004 (1/250914, GnomAD_exome)
G=0.000007 (1/140236, GnomAD)
Clinical Significance
Reported in ClinVar
Gene : Consequence
ACADM : Intron Variant
Publications
1 citation
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.75734878A>G
GRCh38.p13 chr 1 NC_000001.11:g.75734878A>T
GRCh37.p13 chr 1 NC_000001.10:g.76200563A>G
GRCh37.p13 chr 1 NC_000001.10:g.76200563A>T
ACADM RefSeqGene (LRG_838) NG_007045.2:g.15521A>G
ACADM RefSeqGene (LRG_838) NG_007045.2:g.15521A>T
Gene: ACADM, acyl-CoA dehydrogenase medium chain (plus strand)
Molecule type Change Amino acid[Codon] SO Term
ACADM transcript variant 1 NM_000016.6:c.468+7A>G N/A Intron Variant
ACADM transcript variant 3 NM_001127328.3:c.480+7A>G N/A Intron Variant
ACADM transcript variant 4 NM_001286042.2:c.360+7A>G N/A Intron Variant
ACADM transcript variant 5 NM_001286043.2:c.567+7A>G N/A Intron Variant
ACADM transcript variant 6 NM_001286044.2:c.-100+195…

NM_001286044.2:c.-100+1956A>G

N/A Intron 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: 98176 )
ClinVar Accession Disease Names Clinical Significance
RCV000077889.5 not provided Uncertain-Significance
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 250914 A=0.999996 G=0.000004
gnomAD - Exomes European Sub 135070 A=0.999993 G=0.000007
gnomAD - Exomes Asian Sub 48898 A=1.00000 G=0.00000
gnomAD - Exomes American Sub 34534 A=1.00000 G=0.00000
gnomAD - Exomes African Sub 16222 A=1.00000 G=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10066 A=1.00000 G=0.00000
gnomAD - Exomes Other Sub 6124 A=1.0000 G=0.0000
gnomAD - Genomes Global Study-wide 140236 A=0.999993 G=0.000007
gnomAD - Genomes European Sub 75948 A=0.99999 G=0.00001
gnomAD - Genomes African Sub 42038 A=1.00000 G=0.00000
gnomAD - Genomes American Sub 13644 A=1.00000 G=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3322 A=1.0000 G=0.0000
gnomAD - Genomes East Asian Sub 3134 A=1.0000 G=0.0000
gnomAD - Genomes Other Sub 2150 A=1.0000 G=0.0000
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 A= G T
GRCh38.p13 chr 1 NC_000001.11:g.75734878= NC_000001.11:g.75734878A>G NC_000001.11:g.75734878A>T
GRCh37.p13 chr 1 NC_000001.10:g.76200563= NC_000001.10:g.76200563A>G NC_000001.10:g.76200563A>T
ACADM RefSeqGene (LRG_838) NG_007045.2:g.15521= NG_007045.2:g.15521A>G NG_007045.2:g.15521A>T
ACADM transcript variant 1 NM_000016.4:c.468+7= NM_000016.4:c.468+7A>G NM_000016.4:c.468+7A>T
ACADM transcript variant 1 NM_000016.6:c.468+7= NM_000016.6:c.468+7A>G NM_000016.6:c.468+7A>T
ACADM transcript variant 3 NM_001127328.1:c.480+7= NM_001127328.1:c.480+7A>G NM_001127328.1:c.480+7A>T
ACADM transcript variant 3 NM_001127328.3:c.480+7= NM_001127328.3:c.480+7A>G NM_001127328.3:c.480+7A>T
ACADM transcript variant 4 NM_001286042.2:c.360+7= NM_001286042.2:c.360+7A>G NM_001286042.2:c.360+7A>T
ACADM transcript variant 5 NM_001286043.2:c.567+7= NM_001286043.2:c.567+7A>G NM_001286043.2:c.567+7A>T
ACADM transcript variant 6 NM_001286044.2:c.-100+1956= NM_001286044.2:c.-100+1956A>G NM_001286044.2:c.-100+1956A>T
ACADM transcript variant X1 XM_005270811.1:c.360+7= XM_005270811.1:c.360+7A>G XM_005270811.1:c.360+7A>T
ACADM transcript variant X2 XM_005270812.1:c.210+7= XM_005270812.1:c.210+7A>G XM_005270812.1:c.210+7A>T
ACADM transcript variant X3 XM_005270813.1:c.210+7= XM_005270813.1:c.210+7A>G XM_005270813.1:c.210+7A>T
ACADM transcript variant X4 XM_005270814.1:c.78+7= XM_005270814.1:c.78+7A>G XM_005270814.1:c.78+7A>T
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#.

5 SubSNP, 4 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 EGL ss947846729 Jan 23, 2014 (138)
2 EVA_EXAC ss1685603918 Apr 01, 2015 (144)
3 EVA_EXAC ss1685603919 Apr 01, 2015 (144)
4 GNOMAD ss2731585058 Nov 08, 2017 (151)
5 GNOMAD ss3996152992 Apr 25, 2021 (155)
6 ExAC

Submission ignored due to conflicting rows:
Row 4805380 (NC_000001.10:76200562:A:A 115657/115658, NC_000001.10:76200562:A:G 1/115658)
Row 4805381 (NC_000001.10:76200562:A:A 115657/115658, NC_000001.10:76200562:A:T 1/115658)

- Oct 11, 2018 (152)
7 ExAC

Submission ignored due to conflicting rows:
Row 4805380 (NC_000001.10:76200562:A:A 115657/115658, NC_000001.10:76200562:A:G 1/115658)
Row 4805381 (NC_000001.10:76200562:A:A 115657/115658, NC_000001.10:76200562:A:T 1/115658)

- Oct 11, 2018 (152)
8 gnomAD - Genomes NC_000001.11 - 75734878 Apr 25, 2021 (155)
9 gnomAD - Exomes NC_000001.10 - 76200563 Jul 12, 2019 (153)
10 ClinVar RCV000077889.5 Oct 11, 2018 (152)
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
604991, ss1685603918, ss2731585058 NC_000001.10:76200562:A:G NC_000001.11:75734877:A:G (self)
15551431, ss3996152992 NC_000001.11:75734877:A:G NC_000001.11:75734877:A:G
ss1685603919, ss2731585058 NC_000001.10:76200562:A:T NC_000001.11:75734877:A:T (self)
RCV000077889.5, ss947846729 NC_000001.11:75734877:A:T NC_000001.11:75734877:A:T (self)
Help

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

1 citation for rs398123077
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
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