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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.

rs138950

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr22:43182780 (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
G>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.075783 (20059/264690, TOPMED)
A=0.084659 (11869/140198, GnomAD)
A=0.10019 (2801/27956, ALFA) (+ 12 more)
A=0.00006 (1/16760, 8.3KJPN)
A=0.0409 (205/5008, 1000G)
A=0.1415 (634/4480, Estonian)
A=0.1183 (456/3854, ALSPAC)
A=0.1216 (451/3708, TWINSUK)
A=0.133 (133/998, GoNL)
A=0.138 (83/600, NorthernSweden)
A=0.032 (7/216, Qatari)
G=0.45 (20/44, SGDP_PRJ)
A=0.15 (6/40, GENOME_DK)
G=0.50 (6/12, Siberian)
A=0.50 (6/12, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
TTLL12 : 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 22 NC_000022.11:g.43182780G>A
GRCh37.p13 chr 22 NC_000022.10:g.43578786G>A
Gene: TTLL12, tubulin tyrosine ligase like 12 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
TTLL12 transcript NM_015140.4:c.347+200C>T 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 27956 G=0.89981 A=0.10019
European Sub 20418 G=0.87800 A=0.12200
African Sub 5578 G=0.9636 A=0.0364
African Others Sub 198 G=0.975 A=0.025
African American Sub 5380 G=0.9632 A=0.0368
Asian Sub 112 G=1.000 A=0.000
East Asian Sub 86 G=1.00 A=0.00
Other Asian Sub 26 G=1.00 A=0.00
Latin American 1 Sub 146 G=0.925 A=0.075
Latin American 2 Sub 610 G=0.956 A=0.044
South Asian Sub 98 G=0.99 A=0.01
Other Sub 994 G=0.932 A=0.068


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").

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Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 264690 G=0.924217 A=0.075783
gnomAD - Genomes Global Study-wide 140198 G=0.915341 A=0.084659
gnomAD - Genomes European Sub 75908 G=0.88099 A=0.11901
gnomAD - Genomes African Sub 42028 G=0.96352 A=0.03648
gnomAD - Genomes American Sub 13652 G=0.94074 A=0.05926
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=0.8980 A=0.1020
gnomAD - Genomes East Asian Sub 3132 G=0.9997 A=0.0003
gnomAD - Genomes Other Sub 2154 G=0.9290 A=0.0710
8.3KJPN JAPANESE Study-wide 16760 G=0.99994 A=0.00006
1000Genomes Global Study-wide 5008 G=0.9591 A=0.0409
1000Genomes African Sub 1322 G=0.9818 A=0.0182
1000Genomes East Asian Sub 1008 G=0.9990 A=0.0010
1000Genomes Europe Sub 1006 G=0.8688 A=0.1312
1000Genomes South Asian Sub 978 G=0.980 A=0.020
1000Genomes American Sub 694 G=0.960 A=0.040
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.8585 A=0.1415
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.8817 A=0.1183
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.8784 A=0.1216
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.867 A=0.133
Northern Sweden ACPOP Study-wide 600 G=0.862 A=0.138
Qatari Global Study-wide 216 G=0.968 A=0.032
SGDP_PRJ Global Study-wide 44 G=0.45 A=0.55
The Danish reference pan genome Danish Study-wide 40 G=0.85 A=0.15
Siberian Global Study-wide 12 G=0.50 A=0.50
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 G= A
GRCh38.p13 chr 22 NC_000022.11:g.43182780= NC_000022.11:g.43182780G>A
GRCh37.p13 chr 22 NC_000022.10:g.43578786= NC_000022.10:g.43578786G>A
TTLL12 transcript NM_015140.3:c.347+200= NM_015140.3:c.347+200C>T
TTLL12 transcript NM_015140.4:c.347+200= NM_015140.4:c.347+200C>T
TTLL12 transcript variant X1 XM_005261402.1:c.140+200= XM_005261402.1:c.140+200C>T
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#.

43 SubSNP, 14 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC ss147341 Jun 24, 2000 (78)
2 SC_SNP ss8290624 Apr 21, 2003 (114)
3 KRIBB_YJKIM ss80750555 Dec 15, 2007 (130)
4 BCMHGSC_JDW ss91933625 Mar 24, 2008 (129)
5 1000GENOMES ss112678546 Jan 25, 2009 (130)
6 ILLUMINA-UK ss117420180 Feb 14, 2009 (130)
7 ENSEMBL ss138361805 Dec 01, 2009 (131)
8 BCM-HGSC-SUB ss208839839 Jul 04, 2010 (132)
9 1000GENOMES ss238084925 Jul 15, 2010 (132)
10 PJP ss292769791 May 09, 2011 (134)
11 TISHKOFF ss566672737 Apr 25, 2013 (138)
12 SSMP ss662602068 Apr 25, 2013 (138)
13 EVA-GONL ss995402565 Aug 21, 2014 (142)
14 1000GENOMES ss1367370537 Aug 21, 2014 (142)
15 EVA_GENOME_DK ss1579770382 Apr 01, 2015 (144)
16 EVA_UK10K_ALSPAC ss1640100670 Apr 01, 2015 (144)
17 EVA_UK10K_TWINSUK ss1683094703 Apr 01, 2015 (144)
18 EVA_DECODE ss1699473988 Apr 01, 2015 (144)
19 HAMMER_LAB ss1809810695 Sep 08, 2015 (146)
20 WEILL_CORNELL_DGM ss1938970703 Feb 12, 2016 (147)
21 JJLAB ss2030258033 Sep 14, 2016 (149)
22 USC_VALOUEV ss2158879064 Dec 20, 2016 (150)
23 HUMAN_LONGEVITY ss2247752436 Dec 20, 2016 (150)
24 TOPMED ss2414751203 Dec 20, 2016 (150)
25 GNOMAD ss2974994226 Nov 08, 2017 (151)
26 AFFY ss2985240888 Nov 08, 2017 (151)
27 AFFY ss2985858628 Nov 08, 2017 (151)
28 SWEGEN ss3019390380 Nov 08, 2017 (151)
29 BIOINF_KMB_FNS_UNIBA ss3028964885 Nov 08, 2017 (151)
30 CSHL ss3352859580 Nov 08, 2017 (151)
31 TOPMED ss3378569115 Nov 08, 2017 (151)
32 ILLUMINA ss3654009173 Oct 12, 2018 (152)
33 EGCUT_WGS ss3685880579 Jul 13, 2019 (153)
34 EVA_DECODE ss3708304884 Jul 13, 2019 (153)
35 ACPOP ss3743976805 Jul 13, 2019 (153)
36 EVA ss3759444515 Jul 13, 2019 (153)
37 PACBIO ss3788840346 Jul 13, 2019 (153)
38 PACBIO ss3793703203 Jul 13, 2019 (153)
39 PACBIO ss3798589685 Jul 13, 2019 (153)
40 EVA ss3836016979 Apr 27, 2020 (154)
41 SGDP_PRJ ss3890656713 Apr 27, 2020 (154)
42 TOPMED ss5111077209 Apr 26, 2021 (155)
43 TOMMO_GENOMICS ss5232879737 Apr 26, 2021 (155)
44 1000Genomes NC_000022.10 - 43578786 Oct 12, 2018 (152)
45 The Avon Longitudinal Study of Parents and Children NC_000022.10 - 43578786 Oct 12, 2018 (152)
46 Genetic variation in the Estonian population NC_000022.10 - 43578786 Oct 12, 2018 (152)
47 The Danish reference pan genome NC_000022.10 - 43578786 Apr 27, 2020 (154)
48 gnomAD - Genomes NC_000022.11 - 43182780 Apr 26, 2021 (155)
49 Genome of the Netherlands Release 5 NC_000022.10 - 43578786 Apr 27, 2020 (154)
50 Northern Sweden NC_000022.10 - 43578786 Jul 13, 2019 (153)
51 Qatari NC_000022.10 - 43578786 Apr 27, 2020 (154)
52 SGDP_PRJ NC_000022.10 - 43578786 Apr 27, 2020 (154)
53 Siberian NC_000022.10 - 43578786 Apr 27, 2020 (154)
54 8.3KJPN NC_000022.10 - 43578786 Apr 26, 2021 (155)
55 TopMed NC_000022.11 - 43182780 Apr 26, 2021 (155)
56 UK 10K study - Twins NC_000022.10 - 43578786 Oct 12, 2018 (152)
57 ALFA NC_000022.11 - 43182780 Apr 26, 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)
rs58958987 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss91933625, ss112678546, ss117420180, ss208839839, ss292769791, ss1699473988 NC_000022.9:41908729:G:A NC_000022.11:43182779:G:A (self)
80930337, 44766494, 31618827, 5935321, 19943944, 17261670, 21012625, 42673693, 11395418, 90849044, 44766494, ss238084925, ss566672737, ss662602068, ss995402565, ss1367370537, ss1579770382, ss1640100670, ss1683094703, ss1809810695, ss1938970703, ss2030258033, ss2158879064, ss2414751203, ss2974994226, ss2985240888, ss2985858628, ss3019390380, ss3352859580, ss3654009173, ss3685880579, ss3743976805, ss3759444515, ss3788840346, ss3793703203, ss3798589685, ss3836016979, ss3890656713, ss5232879737 NC_000022.10:43578785:G:A NC_000022.11:43182779:G:A (self)
571521032, 241249478, 386186156, 10424142561, ss2247752436, ss3028964885, ss3378569115, ss3708304884, ss5111077209 NC_000022.11:43182779:G:A NC_000022.11:43182779:G:A (self)
ss147341, ss8290624, ss80750555, ss138361805 NT_011520.12:22969354:G:A NC_000022.11:43182779:G:A (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 rs138950

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