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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.

rs544800518

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:597083-597087 (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
delCA / dupCA
Variation Type
Indel Insertion and Deletion
Frequency
delCA=0.001689 (180/106596, GnomAD)
delCA=0.00006 (1/15442, 8.3KJPN)
delCA=0.00152 (18/11862, ALFA) (+ 1 more)
delCA=0.0018 (9/5008, 1000G)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LOC105378947 : Intron Variant
Publications
0 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.597084CA[1]
GRCh38.p13 chr 1 NC_000001.11:g.597084CA[3]
GRCh37.p13 chr 1 NC_000001.10:g.532464CA[1]
GRCh37.p13 chr 1 NC_000001.10:g.532464CA[3]
Gene: LOC105378947, uncharacterized LOC105378947 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC105378947 transcript XM_011542538.1:c.2136+431…

XM_011542538.1:c.2136+4314_2136+4315del

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.

Not Reported in ClinVar

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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 11862 ACACA=0.99848 ACA=0.00152
European Sub 7618 ACACA=0.9979 ACA=0.0021
African Sub 2816 ACACA=0.9993 ACA=0.0007
African Others Sub 108 ACACA=1.000 ACA=0.000
African American Sub 2708 ACACA=0.9993 ACA=0.0007
Asian Sub 108 ACACA=1.000 ACA=0.000
East Asian Sub 84 ACACA=1.00 ACA=0.00
Other Asian Sub 24 ACACA=1.00 ACA=0.00
Latin American 1 Sub 146 ACACA=1.000 ACA=0.000
Latin American 2 Sub 610 ACACA=1.000 ACA=0.000
South Asian Sub 94 ACACA=1.00 ACA=0.00
Other Sub 470 ACACA=1.000 ACA=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
gnomAD - Genomes Global Study-wide 106596 ACACA=0.998311 delCA=0.001689
gnomAD - Genomes European Sub 69006 ACACA=0.99864 delCA=0.00136
gnomAD - Genomes African Sub 18292 ACACA=0.99869 delCA=0.00131
gnomAD - Genomes American Sub 11688 ACACA=0.99683 delCA=0.00317
gnomAD - Genomes Ashkenazi Jewish Sub 3044 ACACA=0.9931 delCA=0.0069
gnomAD - Genomes East Asian Sub 2826 ACACA=1.0000 delCA=0.0000
gnomAD - Genomes Other Sub 1740 ACACA=0.9977 delCA=0.0023
8.3KJPN JAPANESE Study-wide 15442 ACACA=0.99994 delCA=0.00006
1000Genomes Global Study-wide 5008 ACACA=0.9982 delCA=0.0018
1000Genomes African Sub 1322 ACACA=1.0000 delCA=0.0000
1000Genomes East Asian Sub 1008 ACACA=1.0000 delCA=0.0000
1000Genomes Europe Sub 1006 ACACA=0.9990 delCA=0.0010
1000Genomes South Asian Sub 978 ACACA=0.992 delCA=0.008
1000Genomes American Sub 694 ACACA=1.000 delCA=0.000
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 ACACA= delCA dupCA
GRCh38.p13 chr 1 NC_000001.11:g.597083_597087= NC_000001.11:g.597084CA[1] NC_000001.11:g.597084CA[3]
GRCh37.p13 chr 1 NC_000001.10:g.532463_532467= NC_000001.10:g.532464CA[1] NC_000001.10:g.532464CA[3]
LOC105378947 transcript XM_011542538.1:c.2136+4315= XM_011542538.1:c.2136+4314_2136+4315del XM_011542538.1:c.2136+4312GT[3]
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, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss1367645264 Aug 21, 2014 (142)
2 EVA_UK10K_ALSPAC ss1700140454 Apr 01, 2015 (144)
3 EVA_UK10K_TWINSUK ss1700153129 Apr 01, 2015 (144)
4 EVA_UK10K_TWINSUK ss1709905375 Apr 01, 2015 (144)
5 EVA_UK10K_ALSPAC ss1709907294 Apr 01, 2015 (144)
6 PADH-LAB_SPU ss1713846962 Sep 08, 2015 (146)
7 SWEGEN ss2986145195 Nov 08, 2017 (151)
8 TOPMED ss3066361190 Nov 08, 2017 (151)
9 GNOMAD ss3986910526 Apr 25, 2021 (155)
10 TOMMO_GENOMICS ss5142042519 Apr 25, 2021 (155)
11 1000Genomes NC_000001.10 - 532463 Oct 11, 2018 (152)
12 The Avon Longitudinal Study of Parents and Children

Submission ignored due to conflicting rows:
Row 41 (NC_000001.10:532462::AC 2/3854)
Row 42 (NC_000001.10:532462:AC: 4/3854)

- Oct 11, 2018 (152)
13 The Avon Longitudinal Study of Parents and Children

Submission ignored due to conflicting rows:
Row 41 (NC_000001.10:532462::AC 2/3854)
Row 42 (NC_000001.10:532462:AC: 4/3854)

- Oct 11, 2018 (152)
14 gnomAD - Genomes NC_000001.11 - 597083 Apr 25, 2021 (155)
15 8.3KJPN NC_000001.10 - 532463 Apr 25, 2021 (155)
16 UK 10K study - Twins

Submission ignored due to conflicting rows:
Row 41 (NC_000001.10:532462::AC 3/3708)
Row 42 (NC_000001.10:532462:AC: 4/3708)

- Oct 11, 2018 (152)
17 UK 10K study - Twins

Submission ignored due to conflicting rows:
Row 41 (NC_000001.10:532462::AC 3/3708)
Row 42 (NC_000001.10:532462:AC: 4/3708)

- Oct 11, 2018 (152)
18 ALFA NC_000001.11 - 597083 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
1351, 11826, ss1367645264, ss1700140454, ss1700153129, ss1713846962, ss2986145195, ss5142042519 NC_000001.10:532462:AC: NC_000001.11:597082:ACACA:ACA (self)
34373, ss3066361190, ss3986910526 NC_000001.11:597082:AC: NC_000001.11:597082:ACACA:ACA (self)
4891361782 NC_000001.11:597082:ACACA:ACA NC_000001.11:597082:ACACA:ACA
NC_000001.10:532462::AC NC_000001.11:597082:ACACA:ACACACA (self)
ss1709905375, ss1709907294 NC_000001.10:532464::AC NC_000001.11:597082:ACACA:ACACACA (self)
Help

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

No publications for rs544800518

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