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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.

rs55694638

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr16:87842569 (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
C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.254921 (67475/264690, TOPMED)
T=0.254913 (35724/140142, GnomAD)
T=0.20896 (5201/24890, ALFA) (+ 13 more)
C=0.27112 (4544/16760, 8.3KJPN)
T=0.3247 (1626/5008, 1000G)
T=0.3350 (1501/4480, Estonian)
T=0.2561 (987/3854, ALSPAC)
T=0.2683 (995/3708, TWINSUK)
C=0.2447 (717/2930, KOREAN)
T=0.282 (281/998, GoNL)
T=0.317 (190/600, NorthernSweden)
C=0.345 (100/290, SGDP_PRJ)
T=0.111 (24/216, Qatari)
C=0.472 (102/216, Vietnamese)
T=0.33 (13/40, GENOME_DK)
C=0.31 (11/36, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SLC7A5 : 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 16 NC_000016.10:g.87842569C>T
GRCh37.p13 chr 16 NC_000016.9:g.87876175C>T
Gene: SLC7A5, solute carrier family 7 member 5 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
SLC7A5 transcript NM_003486.7:c.665-1414G>A N/A Intron Variant
SLC7A5 transcript variant X3 XM_006721286.3:c.200-1414…

XM_006721286.3:c.200-1414G>A

N/A Intron Variant
SLC7A5 transcript variant X1 XM_017023735.1:c.665-1414…

XM_017023735.1:c.665-1414G>A

N/A Intron Variant
SLC7A5 transcript variant X2 XM_017023736.1:c.539-1414…

XM_017023736.1:c.539-1414G>A

N/A Intron Variant
SLC7A5 transcript variant X4 XM_017023737.2:c.134-1414…

XM_017023737.2:c.134-1414G>A

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 24890 C=0.79104 T=0.20896
European Sub 18122 C=0.77475 T=0.22525
African Sub 2754 C=0.9506 T=0.0494
African Others Sub 116 C=0.948 T=0.052
African American Sub 2638 C=0.9507 T=0.0493
Asian Sub 58 C=0.66 T=0.34
East Asian Sub 44 C=0.66 T=0.34
Other Asian Sub 14 C=0.64 T=0.36
Latin American 1 Sub 172 C=0.855 T=0.145
Latin American 2 Sub 798 C=0.719 T=0.281
South Asian Sub 112 C=0.938 T=0.062
Other Sub 2874 C=0.7540 T=0.2460


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=0.745079 T=0.254921
gnomAD - Genomes Global Study-wide 140142 C=0.745087 T=0.254913
gnomAD - Genomes European Sub 75888 C=0.71599 T=0.28401
gnomAD - Genomes African Sub 42022 C=0.86017 T=0.13983
gnomAD - Genomes American Sub 13646 C=0.62047 T=0.37953
gnomAD - Genomes Ashkenazi Jewish Sub 3320 C=0.8503 T=0.1497
gnomAD - Genomes East Asian Sub 3118 C=0.3409 T=0.6591
gnomAD - Genomes Other Sub 2148 C=0.7374 T=0.2626
8.3KJPN JAPANESE Study-wide 16760 C=0.27112 T=0.72888
1000Genomes Global Study-wide 5008 C=0.6753 T=0.3247
1000Genomes African Sub 1322 C=0.8805 T=0.1195
1000Genomes East Asian Sub 1008 C=0.3492 T=0.6508
1000Genomes Europe Sub 1006 C=0.7316 T=0.2684
1000Genomes South Asian Sub 978 C=0.759 T=0.241
1000Genomes American Sub 694 C=0.559 T=0.441
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.6650 T=0.3350
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.7439 T=0.2561
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.7317 T=0.2683
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.2447 T=0.7553
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.718 T=0.282
Northern Sweden ACPOP Study-wide 600 C=0.683 T=0.317
SGDP_PRJ Global Study-wide 290 C=0.345 T=0.655
Qatari Global Study-wide 216 C=0.889 T=0.111
A Vietnamese Genetic Variation Database Global Study-wide 216 C=0.472 T=0.528
The Danish reference pan genome Danish Study-wide 40 C=0.68 T=0.33
Siberian Global Study-wide 36 C=0.31 T=0.69
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.p13 chr 16 NC_000016.10:g.87842569= NC_000016.10:g.87842569C>T
GRCh37.p13 chr 16 NC_000016.9:g.87876175= NC_000016.9:g.87876175C>T
SLC7A5 transcript NM_003486.5:c.665-1414= NM_003486.5:c.665-1414G>A
SLC7A5 transcript NM_003486.7:c.665-1414= NM_003486.7:c.665-1414G>A
SLC7A5 transcript variant X3 XM_006721286.3:c.200-1414= XM_006721286.3:c.200-1414G>A
SLC7A5 transcript variant X1 XM_017023735.1:c.665-1414= XM_017023735.1:c.665-1414G>A
SLC7A5 transcript variant X2 XM_017023736.1:c.539-1414= XM_017023736.1:c.539-1414G>A
SLC7A5 transcript variant X4 XM_017023737.2:c.134-1414= XM_017023737.2:c.134-1414G>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#.

58 SubSNP, 16 Frequency submissions
No Submitter Submission ID Date (Build)
1 HGSV ss77194581 Dec 06, 2007 (129)
2 HGSV ss81983699 Dec 14, 2007 (130)
3 BGI ss106491056 Feb 04, 2009 (130)
4 1000GENOMES ss109563311 Jan 24, 2009 (130)
5 ILLUMINA ss152536498 Dec 01, 2009 (131)
6 GMI ss157711265 Dec 01, 2009 (131)
7 ILLUMINA ss159102650 Dec 01, 2009 (131)
8 ILLUMINA ss159846009 Dec 01, 2009 (131)
9 ILLUMINA ss168871152 Jul 04, 2010 (132)
10 1000GENOMES ss227408857 Jul 14, 2010 (132)
11 1000GENOMES ss237143683 Jul 15, 2010 (132)
12 1000GENOMES ss243461038 Jul 15, 2010 (132)
13 BL ss255876279 May 09, 2011 (134)
14 GMI ss282649086 May 04, 2012 (137)
15 GMI ss287127952 Apr 25, 2013 (138)
16 PJP ss291901809 May 09, 2011 (134)
17 ILLUMINA ss479154469 Sep 08, 2015 (146)
18 ILLUMINA ss532729398 Sep 08, 2015 (146)
19 TISHKOFF ss565098739 Apr 25, 2013 (138)
20 SSMP ss660876306 Apr 25, 2013 (138)
21 ILLUMINA ss832615446 Aug 21, 2014 (142)
22 ILLUMINA ss833206135 Aug 21, 2014 (142)
23 EVA-GONL ss992808481 Aug 21, 2014 (142)
24 JMKIDD_LAB ss1080856160 Aug 21, 2014 (142)
25 1000GENOMES ss1357470496 Aug 21, 2014 (142)
26 EVA_GENOME_DK ss1578043680 Apr 01, 2015 (144)
27 EVA_UK10K_ALSPAC ss1635079282 Apr 01, 2015 (144)
28 EVA_UK10K_TWINSUK ss1678073315 Apr 01, 2015 (144)
29 EVA_DECODE ss1696851074 Apr 01, 2015 (144)
30 HAMMER_LAB ss1808653094 Sep 08, 2015 (146)
31 WEILL_CORNELL_DGM ss1936246778 Feb 12, 2016 (147)
32 GENOMED ss1968330214 Jul 19, 2016 (147)
33 JJLAB ss2028915004 Sep 14, 2016 (149)
34 USC_VALOUEV ss2157353728 Dec 20, 2016 (150)
35 HUMAN_LONGEVITY ss2214667892 Dec 20, 2016 (150)
36 TOPMED ss2379462320 Dec 20, 2016 (150)
37 SYSTEMSBIOZJU ss2628947475 Nov 08, 2017 (151)
38 GRF ss2701889837 Nov 08, 2017 (151)
39 GNOMAD ss2946446756 Nov 08, 2017 (151)
40 SWEGEN ss3015004599 Nov 08, 2017 (151)
41 BIOINF_KMB_FNS_UNIBA ss3028275552 Nov 08, 2017 (151)
42 TOPMED ss3254447235 Nov 08, 2017 (151)
43 CSHL ss3351595172 Nov 08, 2017 (151)
44 ILLUMINA ss3627598066 Oct 12, 2018 (152)
45 ILLUMINA ss3636349181 Oct 12, 2018 (152)
46 ILLUMINA ss3638142935 Oct 12, 2018 (152)
47 EGCUT_WGS ss3681989986 Jul 13, 2019 (153)
48 EVA_DECODE ss3699860237 Jul 13, 2019 (153)
49 ACPOP ss3741772388 Jul 13, 2019 (153)
50 EVA ss3754315089 Jul 13, 2019 (153)
51 KHV_HUMAN_GENOMES ss3819586452 Jul 13, 2019 (153)
52 EVA ss3834721732 Apr 27, 2020 (154)
53 EVA ss3840968044 Apr 27, 2020 (154)
54 EVA ss3846461607 Apr 27, 2020 (154)
55 SGDP_PRJ ss3885081587 Apr 27, 2020 (154)
56 KRGDB ss3934636658 Apr 27, 2020 (154)
57 TOPMED ss5025904713 Apr 27, 2021 (155)
58 TOMMO_GENOMICS ss5220955438 Apr 27, 2021 (155)
59 1000Genomes NC_000016.9 - 87876175 Oct 12, 2018 (152)
60 The Avon Longitudinal Study of Parents and Children NC_000016.9 - 87876175 Oct 12, 2018 (152)
61 Genetic variation in the Estonian population NC_000016.9 - 87876175 Oct 12, 2018 (152)
62 The Danish reference pan genome NC_000016.9 - 87876175 Apr 27, 2020 (154)
63 gnomAD - Genomes NC_000016.10 - 87842569 Apr 27, 2021 (155)
64 Genome of the Netherlands Release 5 NC_000016.9 - 87876175 Apr 27, 2020 (154)
65 KOREAN population from KRGDB NC_000016.9 - 87876175 Apr 27, 2020 (154)
66 Northern Sweden NC_000016.9 - 87876175 Jul 13, 2019 (153)
67 Qatari NC_000016.9 - 87876175 Apr 27, 2020 (154)
68 SGDP_PRJ NC_000016.9 - 87876175 Apr 27, 2020 (154)
69 Siberian NC_000016.9 - 87876175 Apr 27, 2020 (154)
70 8.3KJPN NC_000016.9 - 87876175 Apr 27, 2021 (155)
71 TopMed NC_000016.10 - 87842569 Apr 27, 2021 (155)
72 UK 10K study - Twins NC_000016.9 - 87876175 Oct 12, 2018 (152)
73 A Vietnamese Genetic Variation Database NC_000016.9 - 87876175 Jul 13, 2019 (153)
74 ALFA NC_000016.10 - 87842569 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)
rs57820310 May 24, 2008 (130)
rs386420627 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss77194581, ss81983699, ss109563311, ss255876279, ss282649086, ss287127952, ss291901809, ss1696851074 NC_000016.8:86433675:C:T NC_000016.10:87842568:C:T (self)
70669449, 39212236, 27728234, 4250645, 17478882, 41814052, 15057253, 18288700, 37098567, 9870082, 78924745, 39212236, 8688798, ss227408857, ss237143683, ss243461038, ss479154469, ss532729398, ss565098739, ss660876306, ss832615446, ss833206135, ss992808481, ss1080856160, ss1357470496, ss1578043680, ss1635079282, ss1678073315, ss1808653094, ss1936246778, ss1968330214, ss2028915004, ss2157353728, ss2379462320, ss2628947475, ss2701889837, ss2946446756, ss3015004599, ss3351595172, ss3627598066, ss3636349181, ss3638142935, ss3681989986, ss3741772388, ss3754315089, ss3834721732, ss3840968044, ss3885081587, ss3934636658, ss5220955438 NC_000016.9:87876174:C:T NC_000016.10:87842568:C:T (self)
498360155, 150662094, 241450374, 3138453539, ss2214667892, ss3028275552, ss3254447235, ss3699860237, ss3819586452, ss3846461607, ss5025904713 NC_000016.10:87842568:C:T NC_000016.10:87842568:C:T (self)
ss106491056, ss152536498, ss157711265, ss159102650, ss159846009, ss168871152 NT_010498.15:41490373:C:T NC_000016.10:87842568: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 rs55694638

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