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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.

rs146049960

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr15:42726314 (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>A / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000042 (11/264690, TOPMED)
T=0.000040 (8/202306, GnomAD_exome)
T=0.000082 (14/171152, ALFA) (+ 6 more)
T=0.000021 (3/140302, GnomAD)
T=0.00004 (3/78700, PAGE_STUDY)
T=0.00011 (5/46456, ExAC)
A=0.00004 (1/28258, 14KJPN)
A=0.00006 (1/16760, 8.3KJPN)
T=0.00023 (3/12970, GO-ESP)
Clinical Significance
Reported in ClinVar
Gene : Consequence
CDAN1 : Missense Variant
Publications
0 citations
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 171274 C=0.999918 T=0.000082
European Sub 146886 C=0.999918 T=0.000082
African Sub 4900 C=1.0000 T=0.0000
African Others Sub 176 C=1.000 T=0.000
African American Sub 4724 C=1.0000 T=0.0000
Asian Sub 6348 C=0.9997 T=0.0003
East Asian Sub 4500 C=0.9998 T=0.0002
Other Asian Sub 1848 C=0.9995 T=0.0005
Latin American 1 Sub 442 C=1.000 T=0.000
Latin American 2 Sub 950 C=1.000 T=0.000
South Asian Sub 280 C=1.000 T=0.000
Other Sub 11468 C=1.00000 T=0.00000


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=0.999958 T=0.000042
gnomAD - Exomes Global Study-wide 202306 C=0.999960 T=0.000040
gnomAD - Exomes European Sub 105278 C=0.999953 T=0.000047
gnomAD - Exomes Asian Sub 41526 C=0.99995 T=0.00005
gnomAD - Exomes American Sub 29156 C=1.00000 T=0.00000
gnomAD - Exomes African Sub 12016 C=0.99992 T=0.00008
gnomAD - Exomes Ashkenazi Jewish Sub 9096 C=1.0000 T=0.0000
gnomAD - Exomes Other Sub 5234 C=1.0000 T=0.0000
Allele Frequency Aggregator Total Global 171152 C=0.999918 T=0.000082
Allele Frequency Aggregator European Sub 146782 C=0.999918 T=0.000082
Allele Frequency Aggregator Other Sub 11464 C=1.00000 T=0.00000
Allele Frequency Aggregator Asian Sub 6348 C=0.9997 T=0.0003
Allele Frequency Aggregator African Sub 4886 C=1.0000 T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 950 C=1.000 T=0.000
Allele Frequency Aggregator Latin American 1 Sub 442 C=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 280 C=1.000 T=0.000
gnomAD - Genomes Global Study-wide 140302 C=0.999979 T=0.000021
gnomAD - Genomes European Sub 75964 C=0.99997 T=0.00003
gnomAD - Genomes African Sub 42064 C=0.99998 T=0.00002
gnomAD - Genomes American Sub 13662 C=1.00000 T=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3324 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3134 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2154 C=1.0000 T=0.0000
The PAGE Study Global Study-wide 78700 C=0.99996 T=0.00004
The PAGE Study AfricanAmerican Sub 32516 C=0.99991 T=0.00009
The PAGE Study Mexican Sub 10810 C=1.00000 T=0.00000
The PAGE Study Asian Sub 8316 C=1.0000 T=0.0000
The PAGE Study PuertoRican Sub 7918 C=1.0000 T=0.0000
The PAGE Study NativeHawaiian Sub 4534 C=1.0000 T=0.0000
The PAGE Study Cuban Sub 4230 C=1.0000 T=0.0000
The PAGE Study Dominican Sub 3828 C=1.0000 T=0.0000
The PAGE Study CentralAmerican Sub 2450 C=1.0000 T=0.0000
The PAGE Study SouthAmerican Sub 1982 C=1.0000 T=0.0000
The PAGE Study NativeAmerican Sub 1260 C=1.0000 T=0.0000
The PAGE Study SouthAsian Sub 856 C=1.000 T=0.000
ExAC Global Study-wide 46456 C=0.99989 T=0.00011
ExAC Europe Sub 25788 C=0.99988 T=0.00012
ExAC Asian Sub 13052 C=0.99992 T=0.00008
ExAC African Sub 4726 C=0.9998 T=0.0002
ExAC American Sub 2510 C=1.0000 T=0.0000
ExAC Other Sub 380 C=1.000 T=0.000
14KJPN JAPANESE Study-wide 28258 C=0.99996 A=0.00004
8.3KJPN JAPANESE Study-wide 16760 C=0.99994 A=0.00006
GO Exome Sequencing Project Global Study-wide 12970 C=0.99977 T=0.00023
GO Exome Sequencing Project European American Sub 8578 C=0.9998 T=0.0002
GO Exome Sequencing Project African American Sub 4392 C=0.9998 T=0.0002
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 15 NC_000015.10:g.42726314C>A
GRCh38.p14 chr 15 NC_000015.10:g.42726314C>T
GRCh37.p13 chr 15 NC_000015.9:g.43018512C>A
GRCh37.p13 chr 15 NC_000015.9:g.43018512C>T
CDAN1 RefSeqGene (LRG_1164) NG_012491.1:g.15906G>T
CDAN1 RefSeqGene (LRG_1164) NG_012491.1:g.15906G>A
Gene: CDAN1, codanin 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
CDAN1 transcript NM_138477.4:c.3200G>T R [CGC] > L [CTC] Coding Sequence Variant
codanin-1 NP_612486.2:p.Arg1067Leu R (Arg) > L (Leu) Missense Variant
CDAN1 transcript NM_138477.4:c.3200G>A R [CGC] > H [CAC] Coding Sequence Variant
codanin-1 NP_612486.2:p.Arg1067His R (Arg) > H (His) Missense Variant
CDAN1 transcript variant X5 XM_047432194.1:c. N/A Genic Downstream Transcript Variant
CDAN1 transcript variant X1 XM_011521270.3:c.3227G>T R [CGC] > L [CTC] Coding Sequence Variant
codanin-1 isoform X1 XP_011519572.1:p.Arg1076L…

XP_011519572.1:p.Arg1076Leu

R (Arg) > L (Leu) Missense Variant
CDAN1 transcript variant X1 XM_011521270.3:c.3227G>A R [CGC] > H [CAC] Coding Sequence Variant
codanin-1 isoform X1 XP_011519572.1:p.Arg1076H…

XP_011519572.1:p.Arg1076His

R (Arg) > H (His) Missense Variant
CDAN1 transcript variant X2 XM_011521271.3:c.3224G>T R [CGC] > L [CTC] Coding Sequence Variant
codanin-1 isoform X2 XP_011519573.1:p.Arg1075L…

XP_011519573.1:p.Arg1075Leu

R (Arg) > L (Leu) Missense Variant
CDAN1 transcript variant X2 XM_011521271.3:c.3224G>A R [CGC] > H [CAC] Coding Sequence Variant
codanin-1 isoform X2 XP_011519573.1:p.Arg1075H…

XP_011519573.1:p.Arg1075His

R (Arg) > H (His) Missense Variant
CDAN1 transcript variant X3 XM_005254176.6:c.3203G>T R [CGC] > L [CTC] Coding Sequence Variant
codanin-1 isoform X3 XP_005254233.1:p.Arg1068L…

XP_005254233.1:p.Arg1068Leu

R (Arg) > L (Leu) Missense Variant
CDAN1 transcript variant X3 XM_005254176.6:c.3203G>A R [CGC] > H [CAC] Coding Sequence Variant
codanin-1 isoform X3 XP_005254233.1:p.Arg1068H…

XP_005254233.1:p.Arg1068His

R (Arg) > H (His) Missense Variant
CDAN1 transcript variant X4 XM_047432193.1:c.3227G>T R [CGC] > L [CTC] Coding Sequence Variant
codanin-1 isoform X4 XP_047288149.1:p.Arg1076L…

XP_047288149.1:p.Arg1076Leu

R (Arg) > L (Leu) Missense Variant
CDAN1 transcript variant X4 XM_047432193.1:c.3227G>A R [CGC] > H [CAC] Coding Sequence Variant
codanin-1 isoform X4 XP_047288149.1:p.Arg1076H…

XP_047288149.1:p.Arg1076His

R (Arg) > H (His) Missense Variant
CDAN1 transcript variant X6 XM_047432195.1:c.2192G>T R [CGC] > L [CTC] Coding Sequence Variant
codanin-1 isoform X6 XP_047288151.1:p.Arg731Leu R (Arg) > L (Leu) Missense Variant
CDAN1 transcript variant X6 XM_047432195.1:c.2192G>A R [CGC] > H [CAC] Coding Sequence Variant
codanin-1 isoform X6 XP_047288151.1:p.Arg731His R (Arg) > H (His) Missense Variant
CDAN1 transcript variant X7 XM_011521274.3:c.2192G>T R [CGC] > L [CTC] Coding Sequence Variant
codanin-1 isoform X6 XP_011519576.1:p.Arg731Leu R (Arg) > L (Leu) Missense Variant
CDAN1 transcript variant X7 XM_011521274.3:c.2192G>A R [CGC] > H [CAC] Coding Sequence Variant
codanin-1 isoform X6 XP_011519576.1:p.Arg731His R (Arg) > H (His) Missense Variant
CDAN1 transcript variant X8 XR_931757.3:n. N/A Genic Downstream 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: 976527 )
ClinVar Accession Disease Names Clinical Significance
RCV001450092.1 Congenital dyserythropoietic anemia, type I Likely-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= A T
GRCh38.p14 chr 15 NC_000015.10:g.42726314= NC_000015.10:g.42726314C>A NC_000015.10:g.42726314C>T
GRCh37.p13 chr 15 NC_000015.9:g.43018512= NC_000015.9:g.43018512C>A NC_000015.9:g.43018512C>T
CDAN1 RefSeqGene (LRG_1164) NG_012491.1:g.15906= NG_012491.1:g.15906G>T NG_012491.1:g.15906G>A
CDAN1 transcript NM_138477.4:c.3200= NM_138477.4:c.3200G>T NM_138477.4:c.3200G>A
CDAN1 transcript NM_138477.3:c.3200= NM_138477.3:c.3200G>T NM_138477.3:c.3200G>A
CDAN1 transcript NM_138477.2:c.3200= NM_138477.2:c.3200G>T NM_138477.2:c.3200G>A
CDAN1 transcript variant X3 XM_005254176.6:c.3203= XM_005254176.6:c.3203G>T XM_005254176.6:c.3203G>A
CDAN1 transcript variant X7 XM_005254176.5:c.3203= XM_005254176.5:c.3203G>T XM_005254176.5:c.3203G>A
CDAN1 transcript variant X3 XM_005254176.4:c.3203= XM_005254176.4:c.3203G>T XM_005254176.4:c.3203G>A
CDAN1 transcript variant X4 XM_005254176.3:c.3203= XM_005254176.3:c.3203G>T XM_005254176.3:c.3203G>A
CDAN1 transcript variant X1 XM_005254176.2:c.3203= XM_005254176.2:c.3203G>T XM_005254176.2:c.3203G>A
CDAN1 transcript variant X1 XM_005254176.1:c.3203= XM_005254176.1:c.3203G>T XM_005254176.1:c.3203G>A
CDAN1 transcript variant X1 XM_011521270.3:c.3227= XM_011521270.3:c.3227G>T XM_011521270.3:c.3227G>A
CDAN1 transcript variant X1 XM_011521270.2:c.3227= XM_011521270.2:c.3227G>T XM_011521270.2:c.3227G>A
CDAN1 transcript variant X1 XM_011521270.1:c.3227= XM_011521270.1:c.3227G>T XM_011521270.1:c.3227G>A
CDAN1 transcript variant X2 XM_011521271.3:c.3224= XM_011521271.3:c.3224G>T XM_011521271.3:c.3224G>A
CDAN1 transcript variant X2 XM_011521271.2:c.3224= XM_011521271.2:c.3224G>T XM_011521271.2:c.3224G>A
CDAN1 transcript variant X2 XM_011521271.1:c.3224= XM_011521271.1:c.3224G>T XM_011521271.1:c.3224G>A
CDAN1 transcript variant X7 XM_011521274.3:c.2192= XM_011521274.3:c.2192G>T XM_011521274.3:c.2192G>A
CDAN1 transcript variant X5 XM_011521274.2:c.2192= XM_011521274.2:c.2192G>T XM_011521274.2:c.2192G>A
CDAN1 transcript variant X6 XM_011521274.1:c.2192= XM_011521274.1:c.2192G>T XM_011521274.1:c.2192G>A
CDAN1 transcript variant X6 XM_047432195.1:c.2192= XM_047432195.1:c.2192G>T XM_047432195.1:c.2192G>A
CDAN1 transcript variant X4 XM_047432193.1:c.3227= XM_047432193.1:c.3227G>T XM_047432193.1:c.3227G>A
codanin-1 NP_612486.2:p.Arg1067= NP_612486.2:p.Arg1067Leu NP_612486.2:p.Arg1067His
codanin-1 isoform X3 XP_005254233.1:p.Arg1068= XP_005254233.1:p.Arg1068Leu XP_005254233.1:p.Arg1068His
codanin-1 isoform X1 XP_011519572.1:p.Arg1076= XP_011519572.1:p.Arg1076Leu XP_011519572.1:p.Arg1076His
codanin-1 isoform X2 XP_011519573.1:p.Arg1075= XP_011519573.1:p.Arg1075Leu XP_011519573.1:p.Arg1075His
codanin-1 isoform X6 XP_011519576.1:p.Arg731= XP_011519576.1:p.Arg731Leu XP_011519576.1:p.Arg731His
codanin-1 isoform X6 XP_047288151.1:p.Arg731= XP_047288151.1:p.Arg731Leu XP_047288151.1:p.Arg731His
codanin-1 isoform X4 XP_047288149.1:p.Arg1076= XP_047288149.1:p.Arg1076Leu XP_047288149.1:p.Arg1076His
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#.

30 SubSNP, 9 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 NHLBI-ESP ss342401400 May 09, 2011 (134)
2 EXOME_CHIP ss491493363 May 04, 2012 (137)
3 ILLUMINA ss780707755 Sep 08, 2015 (146)
4 ILLUMINA ss783382428 Sep 08, 2015 (146)
5 EVA_EXAC ss1691788299 Apr 01, 2015 (144)
6 ILLUMINA ss1752160034 Sep 08, 2015 (146)
7 ILLUMINA ss1917895460 Feb 12, 2016 (147)
8 ILLUMINA ss1946391774 Feb 12, 2016 (147)
9 ILLUMINA ss1959607569 Feb 12, 2016 (147)
10 HUMAN_LONGEVITY ss2206276557 Dec 20, 2016 (150)
11 GNOMAD ss2741182578 Nov 08, 2017 (151)
12 GNOMAD ss2749286709 Nov 08, 2017 (151)
13 GNOMAD ss2934172499 Nov 08, 2017 (151)
14 ILLUMINA ss3021627165 Nov 08, 2017 (151)
15 ILLUMINA ss3627347226 Oct 12, 2018 (152)
16 ILLUMINA ss3634603594 Oct 12, 2018 (152)
17 ILLUMINA ss3640310918 Oct 12, 2018 (152)
18 ILLUMINA ss3644644883 Oct 12, 2018 (152)
19 ILLUMINA ss3652027400 Oct 12, 2018 (152)
20 ILLUMINA ss3725494258 Jul 13, 2019 (153)
21 ILLUMINA ss3744419019 Jul 13, 2019 (153)
22 ILLUMINA ss3744904141 Jul 13, 2019 (153)
23 PAGE_CC ss3771826045 Jul 13, 2019 (153)
24 ILLUMINA ss3772402806 Jul 13, 2019 (153)
25 EVA ss3824911320 Apr 27, 2020 (154)
26 TOPMED ss4989133226 Apr 26, 2021 (155)
27 TOMMO_GENOMICS ss5215897319 Apr 26, 2021 (155)
28 TOMMO_GENOMICS ss5769615025 Oct 16, 2022 (156)
29 EVA ss5847740454 Oct 16, 2022 (156)
30 EVA ss5948784846 Oct 16, 2022 (156)
31 ExAC NC_000015.9 - 43018512 Oct 12, 2018 (152)
32 gnomAD - Genomes NC_000015.10 - 42726314 Apr 26, 2021 (155)
33 gnomAD - Exomes NC_000015.9 - 43018512 Jul 13, 2019 (153)
34 GO Exome Sequencing Project NC_000015.9 - 43018512 Oct 12, 2018 (152)
35 The PAGE Study NC_000015.10 - 42726314 Jul 13, 2019 (153)
36 8.3KJPN NC_000015.9 - 43018512 Apr 26, 2021 (155)
37 14KJPN NC_000015.10 - 42726314 Oct 16, 2022 (156)
38 TopMed NC_000015.10 - 42726314 Apr 26, 2021 (155)
39 ALFA NC_000015.10 - 42726314 Apr 26, 2021 (155)
40 ClinVar RCV001450092.1 Oct 16, 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
73866626, ss5215897319 NC_000015.9:43018511:C:A NC_000015.10:42726313:C:A (self)
103452129, ss5769615025 NC_000015.10:42726313:C:A NC_000015.10:42726313:C:A
2158702, 10445816, 1368594, ss342401400, ss491493363, ss780707755, ss783382428, ss1691788299, ss1752160034, ss1917895460, ss1946391774, ss1959607569, ss2741182578, ss2749286709, ss2934172499, ss3021627165, ss3627347226, ss3634603594, ss3640310918, ss3644644883, ss3652027400, ss3744419019, ss3744904141, ss3772402806, ss3824911320, ss5847740454, ss5948784846 NC_000015.9:43018511:C:T NC_000015.10:42726313:C:T (self)
RCV001450092.1, 467202472, 1047514, 204678886, 9704542365, ss2206276557, ss3725494258, ss3771826045, ss4989133226 NC_000015.10:42726313:C:T NC_000015.10:42726313: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.

No publications for rs146049960

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