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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.

rs5014362

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr16:87829600 (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
T>A / T>C / T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.354558 (93848/264690, TOPMED)
C=0.338585 (47343/139826, GnomAD)
C=0.33520 (11297/33702, ALFA) (+ 15 more)
T=0.28407 (4761/16760, 8.3KJPN)
C=0.4235 (2121/5008, 1000G)
C=0.3297 (1477/4480, Estonian)
C=0.2823 (1088/3854, ALSPAC)
C=0.2918 (1082/3708, TWINSUK)
T=0.2160 (633/2930, KOREAN)
T=0.2254 (413/1832, Korea1K)
C=0.308 (307/998, GoNL)
C=0.360 (216/600, NorthernSweden)
T=0.336 (121/360, SGDP_PRJ)
C=0.310 (67/216, Qatari)
T=0.321 (68/212, Vietnamese)
T=0.50 (20/40, GENOME_DK)
C=0.50 (20/40, GENOME_DK)
T=0.27 (8/30, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SLC7A5 : 500B Downstream 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 16 NC_000016.10:g.87829600T>A
GRCh38.p13 chr 16 NC_000016.10:g.87829600T>C
GRCh38.p13 chr 16 NC_000016.10:g.87829600T>G
GRCh37.p13 chr 16 NC_000016.9:g.87863206T>A
GRCh37.p13 chr 16 NC_000016.9:g.87863206T>C
GRCh37.p13 chr 16 NC_000016.9:g.87863206T>G
Gene: SLC7A5, solute carrier family 7 member 5 (minus strand) : 500B Downstream Variant
Molecule type Change Amino acid[Codon] SO Term
SLC7A5 transcript NM_003486.7:c. N/A Downstream Transcript Variant
SLC7A5 transcript variant X3 XM_006721286.3:c. N/A Downstream Transcript Variant
SLC7A5 transcript variant X1 XM_017023735.1:c. N/A N/A
SLC7A5 transcript variant X2 XM_017023736.1:c. N/A N/A
SLC7A5 transcript variant X4 XM_017023737.2:c. N/A N/A
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 (New)
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 33702 T=0.66480 C=0.33520
European Sub 21442 T=0.70451 C=0.29549
African Sub 3378 T=0.6128 C=0.3872
African Others Sub 132 T=0.644 C=0.356
African American Sub 3246 T=0.6115 C=0.3885
Asian Sub 140 T=0.364 C=0.636
East Asian Sub 108 T=0.380 C=0.620
Other Asian Sub 32 T=0.31 C=0.69
Latin American 1 Sub 302 T=0.632 C=0.368
Latin American 2 Sub 5208 T=0.5301 C=0.4699
South Asian Sub 136 T=0.809 C=0.191
Other Sub 3096 T=0.6835 C=0.3165


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 T=0.645442 C=0.354558
gnomAD - Genomes Global Study-wide 139826 T=0.661415 C=0.338585
gnomAD - Genomes European Sub 75756 T=0.71363 C=0.28637
gnomAD - Genomes African Sub 41858 T=0.61037 C=0.38963
gnomAD - Genomes American Sub 13628 T=0.58637 C=0.41363
gnomAD - Genomes Ashkenazi Jewish Sub 3322 T=0.7757 C=0.2243
gnomAD - Genomes East Asian Sub 3120 T=0.2933 C=0.7067
gnomAD - Genomes Other Sub 2142 T=0.6485 C=0.3515
8.3KJPN JAPANESE Study-wide 16760 T=0.28407 C=0.71593
1000Genomes Global Study-wide 5008 T=0.5765 C=0.4235
1000Genomes African Sub 1322 T=0.5976 C=0.4024
1000Genomes East Asian Sub 1008 T=0.3006 C=0.6994
1000Genomes Europe Sub 1006 T=0.7247 C=0.2753
1000Genomes South Asian Sub 978 T=0.729 C=0.271
1000Genomes American Sub 694 T=0.507 C=0.493
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.6703 C=0.3297
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.7177 C=0.2823
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.7082 C=0.2918
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.2160 A=0.0000, C=0.7840, G=0.0000
Korean Genome Project KOREAN Study-wide 1832 T=0.2254 C=0.7746
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.692 C=0.308
Northern Sweden ACPOP Study-wide 600 T=0.640 C=0.360
SGDP_PRJ Global Study-wide 360 T=0.336 C=0.664
Qatari Global Study-wide 216 T=0.690 C=0.310
A Vietnamese Genetic Variation Database Global Study-wide 212 T=0.321 C=0.679
The Danish reference pan genome Danish Study-wide 40 T=0.50 C=0.50
Siberian Global Study-wide 30 T=0.27 C=0.73
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 T= A C G
GRCh38.p13 chr 16 NC_000016.10:g.87829600= NC_000016.10:g.87829600T>A NC_000016.10:g.87829600T>C NC_000016.10:g.87829600T>G
GRCh37.p13 chr 16 NC_000016.9:g.87863206= NC_000016.9:g.87863206T>A NC_000016.9:g.87863206T>C NC_000016.9:g.87863206T>G
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#.

62 SubSNP, 17 Frequency submissions
No Submitter Submission ID Date (Build)
1 ABI ss43961180 Mar 15, 2006 (126)
2 HGSV ss78325707 Dec 07, 2007 (129)
3 HGSV ss82815584 Dec 15, 2007 (130)
4 1000GENOMES ss109563161 Jan 24, 2009 (130)
5 1000GENOMES ss113144965 Jan 25, 2009 (130)
6 ILLUMINA-UK ss118362048 Feb 14, 2009 (130)
7 ILLUMINA ss152536504 Dec 01, 2009 (131)
8 GMI ss157711110 Dec 01, 2009 (131)
9 ILLUMINA ss159102651 Dec 01, 2009 (131)
10 ILLUMINA ss159846010 Dec 01, 2009 (131)
11 ILLUMINA ss168871165 Jul 04, 2010 (132)
12 COMPLETE_GENOMICS ss170612198 Jul 04, 2010 (132)
13 BCM-HGSC-SUB ss207603872 Jul 04, 2010 (132)
14 1000GENOMES ss227408744 Jul 14, 2010 (132)
15 1000GENOMES ss237143616 Jul 15, 2010 (132)
16 1000GENOMES ss243460987 Jul 15, 2010 (132)
17 BL ss255876207 May 09, 2011 (134)
18 GMI ss282649052 May 04, 2012 (137)
19 GMI ss287127936 Apr 25, 2013 (138)
20 PJP ss291901770 May 09, 2011 (134)
21 ILLUMINA ss479154473 Sep 08, 2015 (146)
22 ILLUMINA ss532729400 Sep 08, 2015 (146)
23 TISHKOFF ss565098609 Apr 25, 2013 (138)
24 SSMP ss660876198 Apr 25, 2013 (138)
25 ILLUMINA ss832615447 Jul 13, 2019 (153)
26 EVA-GONL ss992808315 Aug 21, 2014 (142)
27 JMKIDD_LAB ss1080856054 Aug 21, 2014 (142)
28 1000GENOMES ss1357469870 Aug 21, 2014 (142)
29 EVA_GENOME_DK ss1578043619 Apr 01, 2015 (144)
30 EVA_UK10K_ALSPAC ss1635078992 Apr 01, 2015 (144)
31 EVA_UK10K_TWINSUK ss1678073025 Apr 01, 2015 (144)
32 EVA_DECODE ss1696850913 Apr 01, 2015 (144)
33 HAMMER_LAB ss1808652998 Sep 08, 2015 (146)
34 WEILL_CORNELL_DGM ss1936246599 Feb 12, 2016 (147)
35 GENOMED ss1968330184 Jul 19, 2016 (147)
36 JJLAB ss2028914912 Sep 14, 2016 (149)
37 USC_VALOUEV ss2157353649 Dec 20, 2016 (150)
38 HUMAN_LONGEVITY ss2214666686 Dec 20, 2016 (150)
39 TOPMED ss2379461135 Dec 20, 2016 (150)
40 SYSTEMSBIOZJU ss2628947441 Nov 08, 2017 (151)
41 GRF ss2701889760 Nov 08, 2017 (151)
42 GNOMAD ss2946445265 Nov 08, 2017 (151)
43 SWEGEN ss3015004376 Nov 08, 2017 (151)
44 BIOINF_KMB_FNS_UNIBA ss3028275496 Nov 08, 2017 (151)
45 TOPMED ss3254444021 Nov 08, 2017 (151)
46 CSHL ss3351595106 Nov 08, 2017 (151)
47 ILLUMINA ss3627597990 Oct 12, 2018 (152)
48 ILLUMINA ss3636349144 Oct 12, 2018 (152)
49 ILLUMINA ss3638142898 Oct 12, 2018 (152)
50 EGCUT_WGS ss3681989752 Jul 13, 2019 (153)
51 EVA_DECODE ss3699859924 Jul 13, 2019 (153)
52 ACPOP ss3741772259 Jul 13, 2019 (153)
53 EVA ss3754314893 Jul 13, 2019 (153)
54 KHV_HUMAN_GENOMES ss3819586247 Jul 13, 2019 (153)
55 EVA ss3834721656 Apr 27, 2020 (154)
56 EVA ss3840967988 Apr 27, 2020 (154)
57 EVA ss3846461549 Apr 27, 2020 (154)
58 SGDP_PRJ ss3885081315 Apr 27, 2020 (154)
59 KRGDB ss3934636349 Apr 27, 2020 (154)
60 KOGIC ss3978172775 Apr 27, 2020 (154)
61 TOPMED ss5025900317 Apr 27, 2021 (155)
62 TOMMO_GENOMICS ss5220954817 Apr 27, 2021 (155)
63 1000Genomes NC_000016.9 - 87863206 Oct 12, 2018 (152)
64 The Avon Longitudinal Study of Parents and Children NC_000016.9 - 87863206 Oct 12, 2018 (152)
65 Genetic variation in the Estonian population NC_000016.9 - 87863206 Oct 12, 2018 (152)
66 The Danish reference pan genome NC_000016.9 - 87863206 Apr 27, 2020 (154)
67 gnomAD - Genomes NC_000016.10 - 87829600 Apr 27, 2021 (155)
68 Genome of the Netherlands Release 5 NC_000016.9 - 87863206 Apr 27, 2020 (154)
69 KOREAN population from KRGDB NC_000016.9 - 87863206 Apr 27, 2020 (154)
70 Korean Genome Project NC_000016.10 - 87829600 Apr 27, 2020 (154)
71 Northern Sweden NC_000016.9 - 87863206 Jul 13, 2019 (153)
72 Qatari NC_000016.9 - 87863206 Apr 27, 2020 (154)
73 SGDP_PRJ NC_000016.9 - 87863206 Apr 27, 2020 (154)
74 Siberian NC_000016.9 - 87863206 Apr 27, 2020 (154)
75 8.3KJPN NC_000016.9 - 87863206 Apr 27, 2021 (155)
76 TopMed NC_000016.10 - 87829600 Apr 27, 2021 (155)
77 UK 10K study - Twins NC_000016.9 - 87863206 Oct 12, 2018 (152)
78 A Vietnamese Genetic Variation Database NC_000016.9 - 87863206 Jul 13, 2019 (153)
79 ALFA NC_000016.10 - 87829600 Apr 27, 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).

Associated ID History Updated (Build)
rs59073040 May 25, 2008 (130)
rs386420628 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
41813743, ss3934636349 NC_000016.9:87863205:T:A NC_000016.10:87829599:T:A (self)
ss78325707, ss82815584, ss109563161, ss113144965, ss118362048, ss170612198, ss207603872, ss255876207, ss282649052, ss287127936, ss291901770, ss1696850913 NC_000016.8:86420706:T:C NC_000016.10:87829599:T:C (self)
70668809, 39211924, 27728000, 4250584, 17478718, 41813743, 15057124, 18288521, 37098295, 9870003, 78924124, 39211924, 8688720, ss227408744, ss237143616, ss243460987, ss479154473, ss532729400, ss565098609, ss660876198, ss832615447, ss992808315, ss1080856054, ss1357469870, ss1578043619, ss1635078992, ss1678073025, ss1808652998, ss1936246599, ss1968330184, ss2028914912, ss2157353649, ss2379461135, ss2628947441, ss2701889760, ss2946445265, ss3015004376, ss3351595106, ss3627597990, ss3636349144, ss3638142898, ss3681989752, ss3741772259, ss3754314893, ss3834721656, ss3840967988, ss3885081315, ss3934636349, ss5220954817 NC_000016.9:87863205:T:C NC_000016.10:87829599:T:C (self)
498356589, 34550776, 150659307, 241445978, 10329997765, ss2214666686, ss3028275496, ss3254444021, ss3699859924, ss3819586247, ss3846461549, ss3978172775, ss5025900317 NC_000016.10:87829599:T:C NC_000016.10:87829599:T:C (self)
ss43961180, ss152536504, ss157711110, ss159102651, ss159846010, ss168871165 NT_010498.15:41477404:T:C NC_000016.10:87829599:T:C (self)
41813743, ss3934636349 NC_000016.9:87863205:T:G NC_000016.10:87829599:T:G (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 rs5014362

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