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dbSNP Short Genetic Variations

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.

rs7948623

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr11:61369675 (GRCh38.p12) 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
T=0.06931 (8703/125568, TOPMED)
T=0.101 (505/5008, 1000G)
T=0.005 (22/4480, Estonian) (+ 4 more)
T=0.001 (5/3854, ALSPAC)
T=0.001 (5/3708, TWINSUK)
T=0.00 (0/600, NorthernSweden)
T=0.00 (1/216, Vietnamese)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
TMEM138 : 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.p12 chr 11 NC_000011.10:g.61369675T>A
GRCh38.p12 chr 11 NC_000011.10:g.61369675T>C
GRCh38.p12 chr 11 NC_000011.10:g.61369675T>G
GRCh37.p13 chr 11 NC_000011.9:g.61137147T>A
GRCh37.p13 chr 11 NC_000011.9:g.61137147T>C
GRCh37.p13 chr 11 NC_000011.9:g.61137147T>G
TMEM138 RefSeqGene NG_032581.1:g.12675T>A
TMEM138 RefSeqGene NG_032581.1:g.12675T>C
TMEM138 RefSeqGene NG_032581.1:g.12675T>G
Gene: TMEM138, transmembrane protein 138 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
TMEM138 transcript variant 3 NM_001330281.2:c. N/A Genic Downstream Transcript Variant
TMEM138 transcript variant 1 NM_016464.5:c. N/A Genic Downstream Transcript Variant
TMEM138 transcript variant 2 NR_028473.2:n. N/A Genic Downstream Transcript Variant
TMEM138 transcript variant X6 XM_011545098.2:c. N/A Intron Variant
TMEM138 transcript variant X7 XM_011545099.2:c. N/A Intron Variant
TMEM138 transcript variant X8 XM_011545100.1:c. N/A Intron Variant
TMEM138 transcript variant X9 XM_017017917.1:c. N/A Intron Variant
TMEM138 transcript variant X1 XM_006718585.3:c. N/A Genic Downstream Transcript Variant
TMEM138 transcript variant X2 XM_006718586.2:c. N/A Genic Downstream Transcript Variant
TMEM138 transcript variant X4 XR_949965.1:n. N/A Intron Variant
TMEM138 transcript variant X5 XR_949966.2:n. N/A Intron Variant
TMEM138 transcript variant X3 XR_949964.3: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.

Not Reported in ClinVar
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 125568 T=0.06931 A=0.93069
1000Genomes Global Study-wide 5008 T=0.101 A=0.899
1000Genomes African Sub 1322 T=0.266 A=0.734
1000Genomes East Asian Sub 1008 T=0.003 A=0.997
1000Genomes Europe Sub 1006 T=0.006 A=0.994
1000Genomes South Asian Sub 978 T=0.13 A=0.87
1000Genomes American Sub 694 T=0.03 A=0.97
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.005 A=0.995
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.001 A=0.999
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.001 A=0.999
Northern Sweden ACPOP Study-wide 600 T=0.00 A=1.00
A Vietnamese Genetic Variation Database Global Study-wide 216 T=0.00 A=1.00
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 Note
GRCh38.p12 chr 11 NC_000011.10:...

NC_000011.10:g.61369675=

NC_000011.10:...

NC_000011.10:g.61369675T>A

NC_000011.10:...

NC_000011.10:g.61369675T>C

NC_000011.10:...

NC_000011.10:g.61369675T>G

GRCh37.p13 chr 11 NC_000011.9:g...

NC_000011.9:g.61137147=

NC_000011.9:g...

NC_000011.9:g.61137147T>A

NC_000011.9:g...

NC_000011.9:g.61137147T>C

NC_000011.9:g...

NC_000011.9:g.61137147T>G

TMEM138 RefSeqGene NG_032581.1:g...

NG_032581.1:g.12675=

NG_032581.1:g...

NG_032581.1:g.12675T>A

NG_032581.1:g...

NG_032581.1:g.12675T>C

NG_032581.1:g...

NG_032581.1:g.12675T>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#.

70 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 WI_SSAHASNP ss12166885 Jul 11, 2003 (116)
2 SC_SNP ss15980614 Feb 27, 2004 (120)
3 CSHL-HAPMAP ss17445885 Feb 27, 2004 (120)
4 CSHL-HAPMAP ss19928266 Feb 27, 2004 (120)
5 SSAHASNP ss20837040 Apr 05, 2004 (121)
6 ABI ss40079953 Mar 14, 2006 (126)
7 AFFY ss66272089 Nov 30, 2006 (127)
8 AFFY ss76416801 Dec 08, 2007 (130)
9 HGSV ss81254426 Dec 16, 2007 (130)
10 HGSV ss81722530 Dec 16, 2007 (130)
11 HGSV ss82163378 Dec 16, 2007 (130)
12 KRIBB_YJKIM ss82521476 Dec 15, 2007 (130)
13 HGSV ss84545377 Dec 16, 2007 (130)
14 BCMHGSC_JDW ss88612174 Mar 24, 2008 (129)
15 HUMANGENOME_JCVI ss97390756 Feb 06, 2009 (130)
16 BGI ss106747070 Feb 06, 2009 (130)
17 1000GENOMES ss110553579 Jan 24, 2009 (130)
18 1000GENOMES ss114686915 Jan 25, 2009 (130)
19 ILLUMINA-UK ss119861366 Dec 01, 2009 (131)
20 ENSEMBL ss132592081 Dec 01, 2009 (131)
21 ENSEMBL ss137681841 Dec 01, 2009 (131)
22 GMI ss156382215 Dec 01, 2009 (131)
23 COMPLETE_GENOMICS ss168460223 Jul 04, 2010 (132)
24 COMPLETE_GENOMICS ss170049676 Jul 04, 2010 (132)
25 AFFY ss173517131 Jul 04, 2010 (132)
26 COMPLETE_GENOMICS ss175156523 Jul 04, 2010 (132)
27 BUSHMAN ss202782276 Jul 04, 2010 (132)
28 BCM-HGSC-SUB ss207592178 Jul 04, 2010 (132)
29 1000GENOMES ss225273412 Jul 14, 2010 (132)
30 1000GENOMES ss235584170 Jul 15, 2010 (132)
31 BL ss255213495 May 09, 2011 (134)
32 GMI ss281033973 May 04, 2012 (137)
33 GMI ss286393507 Apr 25, 2013 (138)
34 PJP ss291057737 May 09, 2011 (134)
35 TISHKOFF ss562596758 Apr 25, 2013 (138)
36 SSMP ss658107281 Apr 25, 2013 (138)
37 EVA-GONL ss988584812 Aug 21, 2014 (142)
38 JMKIDD_LAB ss1077775829 Aug 21, 2014 (142)
39 1000GENOMES ss1341512994 Aug 21, 2014 (142)
40 DDI ss1426652019 Apr 01, 2015 (144)
41 EVA_GENOME_DK ss1575747329 Apr 01, 2015 (144)
42 EVA_DECODE ss1598247309 Apr 01, 2015 (144)
43 EVA_UK10K_ALSPAC ss1626715087 Apr 01, 2015 (144)
44 EVA_UK10K_TWINSUK ss1669709120 Apr 01, 2015 (144)
45 EVA_SVP ss1713258567 Apr 01, 2015 (144)
46 HAMMER_LAB ss1806842098 Sep 08, 2015 (146)
47 WEILL_CORNELL_DGM ss1931943902 Feb 12, 2016 (147)
48 GENOMED ss1967376558 Jul 19, 2016 (147)
49 JJLAB ss2026718680 Sep 14, 2016 (149)
50 USC_VALOUEV ss2155021147 Dec 20, 2016 (150)
51 HUMAN_LONGEVITY ss2182818452 Dec 20, 2016 (150)
52 TOPMED ss2346254508 Dec 20, 2016 (150)
53 SYSTEMSBIOZJU ss2627832680 Nov 08, 2017 (151)
54 GRF ss2699310893 Nov 08, 2017 (151)
55 GNOMAD ss2900327724 Nov 08, 2017 (151)
56 SWEGEN ss3008192442 Nov 08, 2017 (151)
57 BIOINF_KMB_FNS_UNIBA ss3027158179 Nov 08, 2017 (151)
58 TOPMED ss3146906808 Nov 08, 2017 (151)
59 TOPMED ss3146906809 Nov 08, 2017 (151)
60 TOPMED ss3146906810 Nov 08, 2017 (151)
61 CSHL ss3349628639 Nov 08, 2017 (151)
62 URBANLAB ss3649624558 Oct 12, 2018 (152)
63 EGCUT_WGS ss3675530627 Jul 13, 2019 (153)
64 EVA_DECODE ss3691900946 Jul 13, 2019 (153)
65 ACPOP ss3738231340 Jul 13, 2019 (153)
66 EVA ss3749370198 Jul 13, 2019 (153)
67 PACBIO ss3786969380 Jul 13, 2019 (153)
68 PACBIO ss3792108641 Jul 13, 2019 (153)
69 PACBIO ss3796990995 Jul 13, 2019 (153)
70 KHV_HUMAN_GENOMES ss3814714326 Jul 13, 2019 (153)
71 1000Genomes NC_000011.9 - 61137147 Oct 12, 2018 (152)
72 The Avon Longitudinal Study of Parents and Children NC_000011.9 - 61137147 Oct 12, 2018 (152)
73 Genetic variation in the Estonian population NC_000011.9 - 61137147 Oct 12, 2018 (152)
74 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 147574865 (NC_000011.9:61137146:T:T 2011/31388, NC_000011.9:61137146:T:A 29377/31388)
Row 147574866 (NC_000011.9:61137146:T:T 31387/31388, NC_000011.9:61137146:T:G 1/31388)

- Jul 13, 2019 (153)
75 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 147574865 (NC_000011.9:61137146:T:T 2011/31388, NC_000011.9:61137146:T:A 29377/31388)
Row 147574866 (NC_000011.9:61137146:T:T 31387/31388, NC_000011.9:61137146:T:G 1/31388)

- Jul 13, 2019 (153)
76 Northern Sweden NC_000011.9 - 61137147 Jul 13, 2019 (153)
77 TopMed NC_000011.10 - 61369675 Oct 12, 2018 (152)
78 UK 10K study - Twins NC_000011.9 - 61137147 Oct 12, 2018 (152)
79 A Vietnamese Genetic Variation Database NC_000011.9 - 61137147 Jul 13, 2019 (153)
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)
rs56531149 May 27, 2008 (130)
rs60356327 Feb 27, 2009 (130)
rs61579951 May 27, 2008 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss66272089, ss76416801, ss81254426, ss81722530, ss82163378, ss84545377, ss88612174, ss110553579, ss114686915, ss119861366, ss168460223, ss170049676, ss173517131, ss175156523, ss202782276, ss207592178, ss255213495, ss281033973, ss286393507, ss291057737, ss1598247309, ss1713258567 NC_000011.8:60893722:T:A NC_000011.10:61369674:T:A (self)
54043704, 30011328, 21268875, 11516205, 30011328, 6663413, ss225273412, ss235584170, ss562596758, ss658107281, ss988584812, ss1077775829, ss1341512994, ss1426652019, ss1575747329, ss1626715087, ss1669709120, ss1806842098, ss1931943902, ss1967376558, ss2026718680, ss2155021147, ss2346254508, ss2627832680, ss2699310893, ss2900327724, ss3008192442, ss3349628639, ss3675530627, ss3738231340, ss3749370198, ss3786969380, ss3792108641, ss3796990995 NC_000011.9:61137146:T:A NC_000011.10:61369674:T:A (self)
64570136, ss2182818452, ss3027158179, ss3146906808, ss3649624558, ss3691900946, ss3814714326 NC_000011.10:61369674:T:A NC_000011.10:61369674:T:A (self)
ss12166885 NT_033903.5:6238413:T:A NC_000011.10:61369674:T:A (self)
ss15980614, ss17445885, ss19928266, ss20837040 NT_033903.6:6310188:T:A NC_000011.10:61369674:T:A (self)
ss40079953, ss82521476, ss97390756, ss106747070, ss132592081, ss137681841, ss156382215 NT_167190.1:6442941:T:A NC_000011.10:61369674:T:A (self)
ss3146906809 NC_000011.10:61369674:T:C NC_000011.10:61369674:T:C (self)
ss2900327724 NC_000011.9:61137146:T:G NC_000011.10:61369674:T:G (self)
ss3146906810 NC_000011.10:61369674:T:G NC_000011.10:61369674: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 rs7948623

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.post104+4a6ee9c