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dbSNP Short Genetic Variations

Reference SNP (rs) Report

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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.

rs119478057

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr16:81264677 (GRCh38.p7) 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>A / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.00136 (336/246268, GnomAD)
T=0.00117 (147/125568, TOPMED)
T=0.00135 (164/121408, ExAC) (+ 4 more)
T=0.0013 (40/30958, GnomAD)
T=0.000 (2/5008, 1000G)
T=0.002 (8/3854, ALSPAC)
T=0.002 (9/3708, TWINSUK)
Clinical Significance
Reported in ClinVar
Gene : Consequence
BCO1 : Missense Variant
Publications
3 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.p7 chr 16 NC_000016.10:g.81264677C>A
GRCh38.p7 chr 16 NC_000016.10:g.81264677C>T
GRCh37.p13 chr 16 NC_000016.9:g.81298282C>A
GRCh37.p13 chr 16 NC_000016.9:g.81298282C>T
BCO1 RefSeqGene NG_012171.1:g.30987C>A
BCO1 RefSeqGene NG_012171.1:g.30987C>T
Gene: BCO1, beta-carotene oxygenase 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
BCO1 transcript NM_017429.2:c.509C>A T [ACG] > K [AAG] Coding Sequence Variant
beta,beta-carotene 15,15'-dioxygenase NP_059125.2:p.Thr...

NP_059125.2:p.Thr170Lys

T (Thr) > K (Lys) Missense Variant
BCO1 transcript NM_017429.2:c.509C>T T [ACG] > M [ATG] Coding Sequence Variant
beta,beta-carotene 15,15'-dioxygenase NP_059125.2:p.Thr...

NP_059125.2:p.Thr170Met

T (Thr) > M (Met) Missense Variant
BCO1 transcript variant X5 XM_017023289.1:c. N/A Genic Upstream Transcript Variant
BCO1 transcript variant X1 XM_011523109.1:c....

XM_011523109.1:c.509C>A

T [ACG] > K [AAG] Coding Sequence Variant
beta,beta-carotene 15,15'-dioxygenase isoform X1 XP_011521411.1:p....

XP_011521411.1:p.Thr170Lys

T (Thr) > K (Lys) Missense Variant
BCO1 transcript variant X1 XM_011523109.1:c....

XM_011523109.1:c.509C>T

T [ACG] > M [ATG] Coding Sequence Variant
beta,beta-carotene 15,15'-dioxygenase isoform X1 XP_011521411.1:p....

XP_011521411.1:p.Thr170Met

T (Thr) > M (Met) Missense Variant
BCO1 transcript variant X2 XM_017023286.1:c....

XM_017023286.1:c.509C>A

T [ACG] > K [AAG] Coding Sequence Variant
beta,beta-carotene 15,15'-dioxygenase isoform X2 XP_016878775.1:p....

XP_016878775.1:p.Thr170Lys

T (Thr) > K (Lys) Missense Variant
BCO1 transcript variant X2 XM_017023286.1:c....

XM_017023286.1:c.509C>T

T [ACG] > M [ATG] Coding Sequence Variant
beta,beta-carotene 15,15'-dioxygenase isoform X2 XP_016878775.1:p....

XP_016878775.1:p.Thr170Met

T (Thr) > M (Met) Missense Variant
BCO1 transcript variant X3 XM_017023287.1:c....

XM_017023287.1:c.509C>A

T [ACG] > K [AAG] Coding Sequence Variant
beta,beta-carotene 15,15'-dioxygenase isoform X3 XP_016878776.1:p....

XP_016878776.1:p.Thr170Lys

T (Thr) > K (Lys) Missense Variant
BCO1 transcript variant X3 XM_017023287.1:c....

XM_017023287.1:c.509C>T

T [ACG] > M [ATG] Coding Sequence Variant
beta,beta-carotene 15,15'-dioxygenase isoform X3 XP_016878776.1:p....

XP_016878776.1:p.Thr170Met

T (Thr) > M (Met) Missense Variant
BCO1 transcript variant X4 XM_017023288.1:c....

XM_017023288.1:c.509C>A

T [ACG] > K [AAG] Coding Sequence Variant
beta,beta-carotene 15,15'-dioxygenase isoform X4 XP_016878777.1:p....

XP_016878777.1:p.Thr170Lys

T (Thr) > K (Lys) Missense Variant
BCO1 transcript variant X4 XM_017023288.1:c....

XM_017023288.1:c.509C>T

T [ACG] > M [ATG] Coding Sequence Variant
beta,beta-carotene 15,15'-dioxygenase isoform X4 XP_016878777.1:p....

XP_016878777.1:p.Thr170Met

T (Thr) > M (Met) Missense Variant
BCO1 transcript variant X6 XR_001751914.1:n....

XR_001751914.1:n.776C>A

N/A Non Coding Transcript Variant
BCO1 transcript variant X6 XR_001751914.1:n....

XR_001751914.1:n.776C>T

N/A Non Coding Transcript 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: 19811 )
ClinVar Accession Disease Names Clinical Significance
RCV000005038.4 Hypercarotenemia and vitamin a deficiency, autosomal dominant Pathogenic
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
The Genome Aggregation Database Global Study-wide 246268 C=0.99863 T=0.00136, A=0.00001
The Genome Aggregation Database European Sub 134018 C=0.99766 T=0.00232, A=0.00001
The Genome Aggregation Database Asian Sub 48028 C=1.0000 T=0.0000, A=0.0000
The Genome Aggregation Database American Sub 33582 C=0.9998 T=0.0002, A=0.0000
The Genome Aggregation Database African Sub 15304 C=0.9996 T=0.0004, A=0.0000
The Genome Aggregation Database Ashkenazi Jewish Sub 9850 C=1.000 T=0.000, A=0.000
The Genome Aggregation Database Other Sub 5486 C=0.999 T=0.001, A=0.000
Trans-Omics for Precision Medicine Global Study-wide 125568 C=0.99881 T=0.00117, A=0.00002
The Exome Aggregation Consortium Global Study-wide 121408 C=0.99865 T=0.00135
The Exome Aggregation Consortium Europe Sub 73350 C=0.9979 T=0.0021
The Exome Aggregation Consortium Asian Sub 25166 C=0.9999 T=0.0001
The Exome Aggregation Consortium American Sub 11578 C=1.0000 T=0.0000
The Exome Aggregation Consortium African Sub 10406 C=0.9994 T=0.0006
The Exome Aggregation Consortium Other Sub 908 C=1.00 T=0.00
The Genome Aggregation Database Global Study-wide 30958 C=0.9987 T=0.0013
The Genome Aggregation Database European Sub 18494 C=0.9980 T=0.0020
The Genome Aggregation Database African Sub 8720 C=1.000 T=0.000
The Genome Aggregation Database East Asian Sub 1622 C=1.000 T=0.000
The Genome Aggregation Database Other Sub 982 C=1.00 T=0.00
The Genome Aggregation Database American Sub 838 C=1.00 T=0.00
The Genome Aggregation Database Ashkenazi Jewish Sub 302 C=1.00 T=0.00
1000Genomes Global Study-wide 5008 C=1.000 T=0.000
1000Genomes African Sub 1322 C=1.000 T=0.000
1000Genomes East Asian Sub 1008 C=1.000 T=0.000
1000Genomes Europe Sub 1006 C=0.998 T=0.002
1000Genomes South Asian Sub 978 C=1.00 T=0.00
1000Genomes American Sub 694 C=1.00 T=0.00
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.998 T=0.002
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.998 T=0.002
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= A T Note
GRCh38.p7 chr 16 NC_000016.10:g.81...

NC_000016.10:g.81264677C=

NC_000016.10:g.81...

NC_000016.10:g.81264677C>A

NC_000016.10:g.81...

NC_000016.10:g.81264677C>T

GRCh37.p13 chr 16 NC_000016.9:g.812...

NC_000016.9:g.81298282C=

NC_000016.9:g.812...

NC_000016.9:g.81298282C>A

NC_000016.9:g.812...

NC_000016.9:g.81298282C>T

BCO1 RefSeqGene NG_012171.1:g.309...

NG_012171.1:g.30987C=

NG_012171.1:g.309...

NG_012171.1:g.30987C>A

NG_012171.1:g.309...

NG_012171.1:g.30987C>T

BCO1 transcript NM_017429.2:c.509C= NM_017429.2:c.509C>A NM_017429.2:c.509C>T
BCO1 transcript variant X3 XM_017023287.1:c....

XM_017023287.1:c.509C=

XM_017023287.1:c....

XM_017023287.1:c.509C>A

XM_017023287.1:c....

XM_017023287.1:c.509C>T

BCO1 transcript variant X6 XR_001751914.1:n....

XR_001751914.1:n.776C=

XR_001751914.1:n....

XR_001751914.1:n.776C>A

XR_001751914.1:n....

XR_001751914.1:n.776C>T

BCO1 transcript variant X1 XM_011523109.1:c....

XM_011523109.1:c.509C=

XM_011523109.1:c....

XM_011523109.1:c.509C>A

XM_011523109.1:c....

XM_011523109.1:c.509C>T

BCO1 transcript variant X2 XM_017023286.1:c....

XM_017023286.1:c.509C=

XM_017023286.1:c....

XM_017023286.1:c.509C>A

XM_017023286.1:c....

XM_017023286.1:c.509C>T

BCO1 transcript variant X4 XM_017023288.1:c....

XM_017023288.1:c.509C=

XM_017023288.1:c....

XM_017023288.1:c.509C>A

XM_017023288.1:c....

XM_017023288.1:c.509C>T

beta,beta-carotene 15,15'-dioxygenase NP_059125.2:p.Thr...

NP_059125.2:p.Thr170=

NP_059125.2:p.Thr...

NP_059125.2:p.Thr170Lys

NP_059125.2:p.Thr...

NP_059125.2:p.Thr170Met

beta,beta-carotene 15,15'-dioxygenase isoform X3 XP_016878776.1:p....

XP_016878776.1:p.Thr170=

XP_016878776.1:p....

XP_016878776.1:p.Thr170Lys

XP_016878776.1:p....

XP_016878776.1:p.Thr170Met

beta,beta-carotene 15,15'-dioxygenase isoform X1 XP_011521411.1:p....

XP_011521411.1:p.Thr170=

XP_011521411.1:p....

XP_011521411.1:p.Thr170Lys

XP_011521411.1:p....

XP_011521411.1:p.Thr170Met

beta,beta-carotene 15,15'-dioxygenase isoform X2 XP_016878775.1:p....

XP_016878775.1:p.Thr170=

XP_016878775.1:p....

XP_016878775.1:p.Thr170Lys

XP_016878775.1:p....

XP_016878775.1:p.Thr170Met

beta,beta-carotene 15,15'-dioxygenase isoform X4 XP_016878777.1:p....

XP_016878777.1:p.Thr170=

XP_016878777.1:p....

XP_016878777.1:p.Thr170Lys

XP_016878777.1:p....

XP_016878777.1:p.Thr170Met

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#.

1 ClinVar, 7 Frequency, 42 SubSNP submissions
No Submitter Submission ID Date (Build)
1 OMIM-CURATED-RECORDS ss254228116 Aug 19, 2010 (132)
2 NHLBI-ESP ss342435037 May 09, 2011 (134)
3 1000GENOMES ss464713037 Sep 17, 2011 (135)
4 1000GENOMES ss491108374 May 04, 2012 (137)
5 EXOME_CHIP ss491512011 May 04, 2012 (137)
6 CLINSEQ_SNP ss491723489 May 04, 2012 (137)
7 ILLUMINA ss780721329 Sep 08, 2015 (146)
8 ILLUMINA ss783396991 Sep 08, 2015 (146)
9 EVA-GONL ss992730366 Aug 21, 2014 (142)
10 1000GENOMES ss1357172353 Aug 21, 2014 (142)
11 EVA_GENOME_DK ss1578009925 Apr 01, 2015 (144)
12 EVA_UK10K_ALSPAC ss1634919316 Apr 01, 2015 (144)
13 EVA_UK10K_TWINSUK ss1677913349 Apr 01, 2015 (144)
14 EVA_EXAC ss1692426380 Apr 01, 2015 (144)
15 EVA_DECODE ss1696770047 Apr 01, 2015 (144)
16 EVA_MGP ss1711437306 Apr 01, 2015 (144)
17 ILLUMINA ss1752206976 Sep 08, 2015 (146)
18 ILLUMINA ss1917910529 Feb 12, 2016 (147)
19 ILLUMINA ss1946421210 Feb 12, 2016 (147)
20 ILLUMINA ss1946421211 Feb 12, 2016 (147)
21 ILLUMINA ss1959700959 Feb 12, 2016 (147)
22 ILLUMINA ss1959700960 Feb 12, 2016 (147)
23 HUMAN_LONGEVITY ss2214068349 Dec 20, 2016 (150)
24 TOPMED ss2378842538 Dec 20, 2016 (150)
25 TOPMED ss2378842539 Dec 20, 2016 (150)
26 ILLUMINA ss2710839086 Nov 08, 2017 (151)
27 GNOMAD ss2742176712 Nov 08, 2017 (151)
28 GNOMAD ss2749601867 Nov 08, 2017 (151)
29 GNOMAD ss2945660011 Nov 08, 2017 (151)
30 AFFY ss2985076580 Nov 08, 2017 (151)
31 SWEGEN ss3014889609 Nov 08, 2017 (151)
32 SWEGEN ss3014889610 Nov 08, 2017 (151)
33 ILLUMINA ss3021730155 Nov 08, 2017 (151)
34 ILLUMINA ss3021730156 Nov 08, 2017 (151)
35 TOPMED ss3252647985 Nov 08, 2017 (151)
36 TOPMED ss3252647986 Nov 08, 2017 (151)
37 ILLUMINA ss3625697332 Jul 20, 2018 (151)
38 ILLUMINA ss3627577319 Jul 20, 2018 (151)
39 ILLUMINA ss3634653073 Jul 20, 2018 (151)
40 ILLUMINA ss3640360393 Jul 20, 2018 (151)
41 ILLUMINA ss3644674306 Jul 20, 2018 (151)
42 ILLUMINA ss3644674307 Jul 20, 2018 (151)
43 1000Genomes NC_000016.9 - 81298282 Jul 20, 2018 (151)
44 The Avon Longitudinal Study of Parents and Children NC_000016.9 - 81298282 Jul 20, 2018 (151)
45 The Exome Aggregation Consortium NC_000016.9 - 81298282 Jul 20, 2018 (151)
46 The Genome Aggregation Database NC_000016.9 - 81298282 Jul 20, 2018 (151)
47 The Genome Aggregation Database NC_000016.9 - 81298282 Jul 20, 2018 (151)
48 Trans-Omics for Precision Medicine NC_000016.10 - 81264677 Jul 20, 2018 (151)
49 UK 10K study - Twins NC_000016.9 - 81298282 Jul 20, 2018 (151)
50 ClinVar RCV000005038.4 Jul 20, 2018 (151)
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
ss491723489, ss1696770047 NC_000016.8:79855782:C= NC_000016.10:81264676:C= (self)
70364490, 39040550, 2842943, 79361538, 11191447, 39040550, ss342435037, ss464713037, ss491108374, ss491512011, ss780721329, ss783396991, ss992730366, ss1357172353, ss1578009925, ss1634919316, ss1677913349, ss1692426380, ss1711437306, ss1752206976, ss1917910529, ss1946421210, ss1946421211, ss1959700959, ss1959700960, ss2378842538, ss2378842539, ss2710839086, ss2742176712, ss2749601867, ss2945660011, ss2985076580, ss3014889609, ss3014889610, ss3021730155, ss3021730156, ss3625697332, ss3627577319, ss3634653073, ss3640360393, ss3644674306, ss3644674307 NC_000016.9:81298281:C= NC_000016.10:81264676:C= (self)
149206437, ss254228116, ss2214068349, ss3252647985, ss3252647986 NC_000016.10:81264676:C= NC_000016.10:81264676:C= (self)
11191447, ss2378842538, ss2742176712, ss3014889610 NC_000016.9:81298281:C>A NC_000016.10:81264676:C>A (self)
149206437, ss3252647985 NC_000016.10:81264676:C>A NC_000016.10:81264676:C>A (self)
ss491723489, ss1696770047 NC_000016.8:79855782:C>T NC_000016.10:81264676:C>T (self)
70364490, 39040550, 2842943, 79361538, 11191447, 39040550, ss342435037, ss464713037, ss491108374, ss491512011, ss780721329, ss783396991, ss992730366, ss1357172353, ss1578009925, ss1634919316, ss1677913349, ss1692426380, ss1711437306, ss1752206976, ss1917910529, ss1946421210, ss1946421211, ss1959700959, ss1959700960, ss2378842539, ss2710839086, ss2742176712, ss2749601867, ss2945660011, ss2985076580, ss3014889609, ss3021730155, ss3021730156, ss3625697332, ss3627577319, ss3634653073, ss3640360393, ss3644674306, ss3644674307 NC_000016.9:81298281:C>T NC_000016.10:81264676:C>T (self)
RCV000005038.4, 149206437, ss254228116, ss2214068349, ss3252647986 NC_000016.10:81264676:C>T NC_000016.10:81264676: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.

3 citations for rs119478057
PMID Title Author Year Journal
5453458 Familial hypercarotinaemia and hypovitaminosis A. Sharvill DE et al. 1970 Proceedings of the Royal Society of Medicine
17951468 Loss-of-function mutation in carotenoid 15,15'-monooxygenase identified in a patient with hypercarotenemia and hypovitaminosis A. Lindqvist A et al. 2007 The Journal of nutrition
27301361 Copy number variation analysis detects novel candidate genes involved in follicular growth and oocyte maturation in a cohort of premature ovarian failure cases. TÅ¡uiko O et al. 2016 Human reproduction (Oxford, England)

Genomic regions, transcripts, and products
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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: 0.1.4.post833+d3ba21e