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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.

rs148059333

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr11:68784814 (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
C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000026 (7/264690, TOPMED)
T=0.000041 (10/245780, GnomAD_exome)
T=0.000050 (7/140238, GnomAD) (+ 3 more)
T=0.000017 (2/117112, ExAC)
T=0.00007 (2/29908, ALFA)
T=0.00008 (1/12988, GO-ESP)
Clinical Significance
Reported in ClinVar
Gene : Consequence
CPT1A : Splice Donor 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 29908 C=0.99993 T=0.00007
European Sub 21894 C=0.99995 T=0.00005
African Sub 3918 C=0.9997 T=0.0003
African Others Sub 122 C=1.000 T=0.000
African American Sub 3796 C=0.9997 T=0.0003
Asian Sub 168 C=1.000 T=0.000
East Asian Sub 112 C=1.000 T=0.000
Other Asian Sub 56 C=1.00 T=0.00
Latin American 1 Sub 146 C=1.000 T=0.000
Latin American 2 Sub 610 C=1.000 T=0.000
South Asian Sub 98 C=1.00 T=0.00
Other Sub 3074 C=1.0000 T=0.0000


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 C=0.999974 T=0.000026
gnomAD - Exomes Global Study-wide 245780 C=0.999959 T=0.000041
gnomAD - Exomes European Sub 130142 C=1.000000 T=0.000000
gnomAD - Exomes Asian Sub 48900 C=1.00000 T=0.00000
gnomAD - Exomes American Sub 34524 C=1.00000 T=0.00000
gnomAD - Exomes African Sub 16110 C=1.00000 T=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10034 C=0.99910 T=0.00090
gnomAD - Exomes Other Sub 6070 C=0.9998 T=0.0002
gnomAD - Genomes Global Study-wide 140238 C=0.999950 T=0.000050
gnomAD - Genomes European Sub 75950 C=0.99999 T=0.00001
gnomAD - Genomes African Sub 42034 C=1.00000 T=0.00000
gnomAD - Genomes American Sub 13648 C=1.00000 T=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3324 C=0.9982 T=0.0018
gnomAD - Genomes East Asian Sub 3130 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2152 C=1.0000 T=0.0000
ExAC Global Study-wide 117112 C=0.999983 T=0.000017
ExAC Europe Sub 70302 C=0.99997 T=0.00003
ExAC Asian Sub 24772 C=1.00000 T=0.00000
ExAC American Sub 11358 C=1.00000 T=0.00000
ExAC African Sub 9838 C=1.0000 T=0.0000
ExAC Other Sub 842 C=1.000 T=0.000
Allele Frequency Aggregator Total Global 29908 C=0.99993 T=0.00007
Allele Frequency Aggregator European Sub 21894 C=0.99995 T=0.00005
Allele Frequency Aggregator African Sub 3918 C=0.9997 T=0.0003
Allele Frequency Aggregator Other Sub 3074 C=1.0000 T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 C=1.000 T=0.000
Allele Frequency Aggregator Asian Sub 168 C=1.000 T=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 C=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 98 C=1.00 T=0.00
GO Exome Sequencing Project Global Study-wide 12988 C=0.99992 T=0.00008
GO Exome Sequencing Project European American Sub 8588 C=0.9999 T=0.0001
GO Exome Sequencing Project African American Sub 4400 C=1.0000 T=0.0000
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.p14 chr 11 NC_000011.10:g.68784814C>T
GRCh37.p13 chr 11 NC_000011.9:g.68552282C>T
CPT1A RefSeqGene NG_011801.1:g.62118G>A
Gene: CPT1A, carnitine palmitoyltransferase 1A (minus strand)
Molecule type Change Amino acid[Codon] SO Term
CPT1A transcript variant 2 NM_001031847.3:c. N/A Splice Donor Variant
CPT1A transcript variant 1 NM_001876.4:c. N/A Splice Donor Variant
CPT1A transcript variant X3 XM_017017220.2:c. N/A Splice Donor Variant
CPT1A transcript variant X1 XM_047426376.1:c. N/A Splice Donor Variant
CPT1A transcript variant X2 XM_047426377.1:c. N/A Splice Donor 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: 358057 )
ClinVar Accession Disease Names Clinical Significance
RCV000548200.11 Carnitine palmitoyl transferase 1A deficiency Pathogenic
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= T
GRCh38.p14 chr 11 NC_000011.10:g.68784814= NC_000011.10:g.68784814C>T
GRCh37.p13 chr 11 NC_000011.9:g.68552282= NC_000011.9:g.68552282C>T
CPT1A RefSeqGene NG_011801.1:g.62118= NG_011801.1:g.62118G>A
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#.

12 SubSNP, 6 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 NHLBI-ESP ss342334405 May 09, 2011 (134)
2 EVA_EXAC ss1690515895 Apr 01, 2015 (144)
3 GNOMAD ss2739200231 Nov 08, 2017 (151)
4 AFFY ss2984948005 Nov 08, 2017 (151)
5 ILLUMINA ss3021348780 Nov 08, 2017 (151)
6 ILLUMINA ss3651713753 Oct 12, 2018 (152)
7 ILLUMINA ss3653720478 Oct 12, 2018 (152)
8 EVA_DECODE ss3692003551 Jul 13, 2019 (153)
9 ILLUMINA ss3725251826 Jul 13, 2019 (153)
10 EVA ss3824647276 Apr 26, 2020 (154)
11 GNOMAD ss4237050914 Apr 26, 2021 (155)
12 TOPMED ss4889201514 Apr 26, 2021 (155)
13 ExAC NC_000011.9 - 68552282 Oct 12, 2018 (152)
14 gnomAD - Genomes NC_000011.10 - 68784814 Apr 26, 2021 (155)
15 gnomAD - Exomes NC_000011.9 - 68552282 Jul 13, 2019 (153)
16 GO Exome Sequencing Project NC_000011.9 - 68552282 Oct 12, 2018 (152)
17 TopMed NC_000011.10 - 68784814 Apr 26, 2021 (155)
18 ALFA NC_000011.10 - 68784814 Apr 26, 2021 (155)
19 ClinVar RCV000548200.11 Oct 17, 2022 (156)
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
782373, 8416182, 1104847, ss342334405, ss1690515895, ss2739200231, ss2984948005, ss3021348780, ss3651713753, ss3653720478, ss3824647276 NC_000011.9:68552281:C:T NC_000011.10:68784813:C:T (self)
RCV000548200.11, 383045670, 104747170, 1619954945, ss3692003551, ss3725251826, ss4237050914, ss4889201514 NC_000011.10:68784813:C:T NC_000011.10:68784813: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.

1 citation for rs148059333
PMID Title Author Year Journal
27066452 Novel Mutations in the CPT1A Gene Identified in the Patient Presenting Jaundice as the First Manifestation of Carnitine Palmitoyltransferase 1A Deficiency. Choi JS et al. 2016 Pediatric gastroenterology, hepatology & nutrition
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.post761+d5e8e07