Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs116647652

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr8:93786285 (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=0.000008 (2/264690, TOPMED)
T=0.000008 (2/251374, GnomAD_exome)
T=0.000007 (1/140116, GnomAD) (+ 5 more)
T=0.000008 (1/121008, ExAC)
T=0.00004 (1/28258, 14KJPN)
T=0.00000 (0/14528, ALFA)
T=0.0002 (1/6404, 1000G_30x)
T=0.0002 (1/5008, 1000G)
Clinical Significance
Reported in ClinVar
Gene : Consequence
TMEM67 : Stop Gained
Publications
1 citation
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 14528 C=1.00000 T=0.00000
European Sub 9690 C=1.0000 T=0.0000
African Sub 3324 C=1.0000 T=0.0000
African Others Sub 114 C=1.000 T=0.000
African American Sub 3210 C=1.0000 T=0.0000
Asian Sub 112 C=1.000 T=0.000
East Asian Sub 86 C=1.00 T=0.00
Other Asian Sub 26 C=1.00 T=0.00
Latin American 1 Sub 146 C=1.000 T=0.000
Latin American 2 Sub 610 C=1.000 T=0.000
South Asian Sub 98 C=1.00 T=0.00
Other Sub 548 C=1.000 T=0.000


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=0.999992 T=0.000008
gnomAD - Exomes Global Study-wide 251374 C=0.999992 T=0.000008
gnomAD - Exomes European Sub 135344 C=1.000000 T=0.000000
gnomAD - Exomes Asian Sub 48990 C=0.99998 T=0.00002
gnomAD - Exomes American Sub 34586 C=0.99997 T=0.00003
gnomAD - Exomes African Sub 16246 C=1.00000 T=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10076 C=1.00000 T=0.00000
gnomAD - Exomes Other Sub 6132 C=1.0000 T=0.0000
gnomAD - Genomes Global Study-wide 140116 C=0.999993 T=0.000007
gnomAD - Genomes European Sub 75898 C=1.00000 T=0.00000
gnomAD - Genomes African Sub 41982 C=1.00000 T=0.00000
gnomAD - Genomes American Sub 13638 C=0.99993 T=0.00007
gnomAD - Genomes Ashkenazi Jewish Sub 3320 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3128 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2150 C=1.0000 T=0.0000
ExAC Global Study-wide 121008 C=0.999992 T=0.000008
ExAC Europe Sub 73196 C=1.00000 T=0.00000
ExAC Asian Sub 25062 C=0.99996 T=0.00004
ExAC American Sub 11518 C=1.00000 T=0.00000
ExAC African Sub 10324 C=1.00000 T=0.00000
ExAC Other Sub 908 C=1.000 T=0.000
14KJPN JAPANESE Study-wide 28258 C=0.99996 T=0.00004
Allele Frequency Aggregator Total Global 14528 C=1.00000 T=0.00000
Allele Frequency Aggregator European Sub 9690 C=1.0000 T=0.0000
Allele Frequency Aggregator African Sub 3324 C=1.0000 T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 C=1.000 T=0.000
Allele Frequency Aggregator Other Sub 548 C=1.000 T=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 C=1.000 T=0.000
Allele Frequency Aggregator Asian Sub 112 C=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 98 C=1.00 T=0.00
1000Genomes_30x Global Study-wide 6404 C=0.9998 T=0.0002
1000Genomes_30x African Sub 1786 C=1.0000 T=0.0000
1000Genomes_30x Europe Sub 1266 C=1.0000 T=0.0000
1000Genomes_30x South Asian Sub 1202 C=1.0000 T=0.0000
1000Genomes_30x East Asian Sub 1170 C=0.9991 T=0.0009
1000Genomes_30x American Sub 980 C=1.000 T=0.000
1000Genomes Global Study-wide 5008 C=0.9998 T=0.0002
1000Genomes African Sub 1322 C=1.0000 T=0.0000
1000Genomes East Asian Sub 1008 C=0.9990 T=0.0010
1000Genomes Europe Sub 1006 C=1.0000 T=0.0000
1000Genomes South Asian Sub 978 C=1.000 T=0.000
1000Genomes American Sub 694 C=1.000 T=0.000
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 8 NC_000008.11:g.93786285C>A
GRCh38.p14 chr 8 NC_000008.11:g.93786285C>T
GRCh37.p13 chr 8 NC_000008.10:g.94798513C>A
GRCh37.p13 chr 8 NC_000008.10:g.94798513C>T
TMEM67 RefSeqGene (LRG_688) NG_009190.1:g.36442C>A
TMEM67 RefSeqGene (LRG_688) NG_009190.1:g.36442C>T
Gene: TMEM67, transmembrane protein 67 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
TMEM67 transcript variant 2 NM_001142301.1:c.1108C>A R [CGA] > R [AGA] Coding Sequence Variant
meckelin isoform 2 NP_001135773.1:p.Arg370= R (Arg) > R (Arg) Synonymous Variant
TMEM67 transcript variant 2 NM_001142301.1:c.1108C>T R [CGA] > * [TGA] Coding Sequence Variant
meckelin isoform 2 NP_001135773.1:p.Arg370Ter R (Arg) > * (Ter) Stop Gained
TMEM67 transcript variant 1 NM_153704.6:c.1351C>A R [CGA] > R [AGA] Coding Sequence Variant
meckelin isoform 1 precursor NP_714915.3:p.Arg451= R (Arg) > R (Arg) Synonymous Variant
TMEM67 transcript variant 1 NM_153704.6:c.1351C>T R [CGA] > * [TGA] Coding Sequence Variant
meckelin isoform 1 precursor NP_714915.3:p.Arg451Ter R (Arg) > * (Ter) Stop Gained
TMEM67 transcript variant 3 NR_024522.2:n.1372C>A N/A Non Coding Transcript Variant
TMEM67 transcript variant 3 NR_024522.2:n.1372C>T N/A Non Coding Transcript Variant
TMEM67 transcript variant X8 XM_006716686.5:c.1048C>A R [CGA] > R [AGA] Coding Sequence Variant
meckelin isoform X1 XP_006716749.1:p.Arg350= R (Arg) > R (Arg) Synonymous Variant
TMEM67 transcript variant X8 XM_006716686.5:c.1048C>T R [CGA] > * [TGA] Coding Sequence Variant
meckelin isoform X1 XP_006716749.1:p.Arg350Ter R (Arg) > * (Ter) Stop Gained
TMEM67 transcript variant X9 XM_047422409.1:c.697C>A R [CGA] > R [AGA] Coding Sequence Variant
meckelin isoform X2 XP_047278365.1:p.Arg233= R (Arg) > R (Arg) Synonymous Variant
TMEM67 transcript variant X9 XM_047422409.1:c.697C>T R [CGA] > * [TGA] Coding Sequence Variant
meckelin isoform X2 XP_047278365.1:p.Arg233Ter R (Arg) > * (Ter) Stop Gained
TMEM67 transcript variant X10 XM_011517363.4:c.469C>A R [CGA] > R [AGA] Coding Sequence Variant
meckelin isoform X3 XP_011515665.1:p.Arg157= R (Arg) > R (Arg) Synonymous Variant
TMEM67 transcript variant X10 XM_011517363.4:c.469C>T R [CGA] > * [TGA] Coding Sequence Variant
meckelin isoform X3 XP_011515665.1:p.Arg157Ter R (Arg) > * (Ter) Stop Gained
TMEM67 transcript variant X11 XM_047422410.1:c.166C>A R [CGA] > R [AGA] Coding Sequence Variant
meckelin isoform X4 XP_047278366.1:p.Arg56= R (Arg) > R (Arg) Synonymous Variant
TMEM67 transcript variant X11 XM_047422410.1:c.166C>T R [CGA] > * [TGA] Coding Sequence Variant
meckelin isoform X4 XP_047278366.1:p.Arg56Ter R (Arg) > * (Ter) Stop Gained
TMEM67 transcript variant X1 XR_428387.3:n.1372C>A N/A Non Coding Transcript Variant
TMEM67 transcript variant X1 XR_428387.3:n.1372C>T N/A Non Coding Transcript Variant
TMEM67 transcript variant X2 XR_928360.4:n.1372C>A N/A Non Coding Transcript Variant
TMEM67 transcript variant X2 XR_928360.4:n.1372C>T N/A Non Coding Transcript Variant
TMEM67 transcript variant X3 XR_001745619.3:n.1372C>A N/A Non Coding Transcript Variant
TMEM67 transcript variant X3 XR_001745619.3:n.1372C>T N/A Non Coding Transcript Variant
TMEM67 transcript variant X4 XR_007060760.1:n.1372C>A N/A Non Coding Transcript Variant
TMEM67 transcript variant X4 XR_007060760.1:n.1372C>T N/A Non Coding Transcript Variant
TMEM67 transcript variant X5 XR_007060761.1:n.1372C>A N/A Non Coding Transcript Variant
TMEM67 transcript variant X5 XR_007060761.1:n.1372C>T N/A Non Coding Transcript Variant
TMEM67 transcript variant X6 XR_007060762.1:n.1372C>A N/A Non Coding Transcript Variant
TMEM67 transcript variant X6 XR_007060762.1:n.1372C>T N/A Non Coding Transcript Variant
TMEM67 transcript variant X7 XR_007060763.1:n.1372C>A N/A Non Coding Transcript Variant
TMEM67 transcript variant X7 XR_007060763.1:n.1372C>T N/A Non Coding 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: A (allele ID: 370398 )
ClinVar Accession Disease Names Clinical Significance
RCV000429502.1 not specified Likely-Benign
Allele: T (allele ID: 214283 )
ClinVar Accession Disease Names Clinical Significance
RCV000201701.3 Joubert syndrome 6 Pathogenic
RCV001536330.2 not provided Pathogenic
RCV001853243.1 Joubert syndrome,Meckel-Gruber syndrome 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 8 NC_000008.11:g.93786285= NC_000008.11:g.93786285C>A NC_000008.11:g.93786285C>T
GRCh37.p13 chr 8 NC_000008.10:g.94798513= NC_000008.10:g.94798513C>A NC_000008.10:g.94798513C>T
TMEM67 RefSeqGene (LRG_688) NG_009190.1:g.36442= NG_009190.1:g.36442C>A NG_009190.1:g.36442C>T
TMEM67 transcript variant 1 NM_153704.6:c.1351= NM_153704.6:c.1351C>A NM_153704.6:c.1351C>T
TMEM67 transcript variant 1 NM_153704.5:c.1351= NM_153704.5:c.1351C>A NM_153704.5:c.1351C>T
TMEM67 transcript variant 3 NR_024522.2:n.1372= NR_024522.2:n.1372C>A NR_024522.2:n.1372C>T
TMEM67 transcript variant 3 NR_024522.1:n.1422= NR_024522.1:n.1422C>A NR_024522.1:n.1422C>T
TMEM67 transcript variant 2 NM_001142301.1:c.1108= NM_001142301.1:c.1108C>A NM_001142301.1:c.1108C>T
TMEM67 transcript variant X8 XM_006716686.5:c.1048= XM_006716686.5:c.1048C>A XM_006716686.5:c.1048C>T
TMEM67 transcript variant X5 XM_006716686.4:c.1048= XM_006716686.4:c.1048C>A XM_006716686.4:c.1048C>T
TMEM67 transcript variant X5 XM_006716686.3:c.1048= XM_006716686.3:c.1048C>A XM_006716686.3:c.1048C>T
TMEM67 transcript variant X5 XM_006716686.2:c.1048= XM_006716686.2:c.1048C>A XM_006716686.2:c.1048C>T
TMEM67 transcript variant X2 XM_006716686.1:c.1048= XM_006716686.1:c.1048C>A XM_006716686.1:c.1048C>T
TMEM67 transcript variant X2 XR_928360.4:n.1372= XR_928360.4:n.1372C>A XR_928360.4:n.1372C>T
TMEM67 transcript variant X1 XR_928360.3:n.1392= XR_928360.3:n.1392C>A XR_928360.3:n.1392C>T
TMEM67 transcript variant X1 XR_928360.2:n.1409= XR_928360.2:n.1409C>A XR_928360.2:n.1409C>T
TMEM67 transcript variant X1 XR_928360.1:n.1409= XR_928360.1:n.1409C>A XR_928360.1:n.1409C>T
TMEM67 transcript variant X10 XM_011517363.4:c.469= XM_011517363.4:c.469C>A XM_011517363.4:c.469C>T
TMEM67 transcript variant X7 XM_011517363.3:c.469= XM_011517363.3:c.469C>A XM_011517363.3:c.469C>T
TMEM67 transcript variant X6 XM_011517363.2:c.469= XM_011517363.2:c.469C>A XM_011517363.2:c.469C>T
TMEM67 transcript variant X7 XM_011517363.1:c.469= XM_011517363.1:c.469C>A XM_011517363.1:c.469C>T
TMEM67 transcript variant X3 XR_001745619.3:n.1372= XR_001745619.3:n.1372C>A XR_001745619.3:n.1372C>T
TMEM67 transcript variant X2 XR_001745619.2:n.1392= XR_001745619.2:n.1392C>A XR_001745619.2:n.1392C>T
TMEM67 transcript variant X2 XR_001745619.1:n.1409= XR_001745619.1:n.1409C>A XR_001745619.1:n.1409C>T
TMEM67 transcript variant X1 XR_428387.3:n.1372= XR_428387.3:n.1372C>A XR_428387.3:n.1372C>T
TMEM67 transcript variant X3 XR_428387.2:n.1392= XR_428387.2:n.1392C>A XR_428387.2:n.1392C>T
TMEM67 transcript variant X3 XR_428387.1:n.1409= XR_428387.1:n.1409C>A XR_428387.1:n.1409C>T
TMEM67 transcript variant X5 XR_007060761.1:n.1372= XR_007060761.1:n.1372C>A XR_007060761.1:n.1372C>T
TMEM67 transcript variant X6 XR_007060762.1:n.1372= XR_007060762.1:n.1372C>A XR_007060762.1:n.1372C>T
TMEM67 transcript variant X4 XR_007060760.1:n.1372= XR_007060760.1:n.1372C>A XR_007060760.1:n.1372C>T
TMEM67 transcript variant X9 XM_047422409.1:c.697= XM_047422409.1:c.697C>A XM_047422409.1:c.697C>T
TMEM67 transcript variant X11 XM_047422410.1:c.166= XM_047422410.1:c.166C>A XM_047422410.1:c.166C>T
TMEM67 transcript variant X7 XR_007060763.1:n.1372= XR_007060763.1:n.1372C>A XR_007060763.1:n.1372C>T
meckelin isoform 1 precursor NP_714915.3:p.Arg451= NP_714915.3:p.Arg451= NP_714915.3:p.Arg451Ter
meckelin isoform 2 NP_001135773.1:p.Arg370= NP_001135773.1:p.Arg370= NP_001135773.1:p.Arg370Ter
meckelin isoform X1 XP_006716749.1:p.Arg350= XP_006716749.1:p.Arg350= XP_006716749.1:p.Arg350Ter
meckelin isoform X3 XP_011515665.1:p.Arg157= XP_011515665.1:p.Arg157= XP_011515665.1:p.Arg157Ter
meckelin isoform X2 XP_047278365.1:p.Arg233= XP_047278365.1:p.Arg233= XP_047278365.1:p.Arg233Ter
meckelin isoform X4 XP_047278366.1:p.Arg56= XP_047278366.1:p.Arg56= XP_047278366.1:p.Arg56Ter
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#.

18 SubSNP, 8 Frequency, 4 ClinVar submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss217407529 Jul 14, 2010 (132)
2 1000GENOMES ss335057951 May 09, 2011 (134)
3 1000GENOMES ss490967416 May 04, 2012 (137)
4 1000GENOMES ss1330988476 Aug 21, 2014 (142)
5 EVA_EXAC ss1689252901 Apr 01, 2015 (144)
6 CLINVAR ss2137502343 Apr 13, 2017 (150)
7 CLINVAR ss2137508694 Apr 18, 2017 (150)
8 GNOMAD ss2737247537 Nov 08, 2017 (151)
9 ILLUMINA ss3022864395 Nov 08, 2017 (151)
10 ILLUMINA ss3653409452 Oct 12, 2018 (152)
11 ILLUMINA ss3726554850 Jul 13, 2019 (153)
12 EVA ss3768333465 Jul 13, 2019 (153)
13 GNOMAD ss4189384170 Apr 26, 2021 (155)
14 TOPMED ss4796134634 Apr 26, 2021 (155)
15 EVA ss5382968509 Oct 16, 2022 (156)
16 1000G_HIGH_COVERAGE ss5569038253 Oct 16, 2022 (156)
17 TOMMO_GENOMICS ss5732391222 Oct 16, 2022 (156)
18 EVA ss5890098127 Oct 16, 2022 (156)
19 1000Genomes NC_000008.10 - 94798513 Oct 12, 2018 (152)
20 1000Genomes_30x NC_000008.11 - 93786285 Oct 16, 2022 (156)
21 ExAC NC_000008.10 - 94798513 Oct 12, 2018 (152)
22 gnomAD - Genomes NC_000008.11 - 93786285 Apr 26, 2021 (155)
23 gnomAD - Exomes NC_000008.10 - 94798513 Jul 13, 2019 (153)
24 14KJPN NC_000008.11 - 93786285 Oct 16, 2022 (156)
25 TopMed NC_000008.11 - 93786285 Apr 26, 2021 (155)
26 ALFA NC_000008.11 - 93786285 Apr 26, 2021 (155)
27 ClinVar RCV000201701.3 Apr 26, 2021 (155)
28 ClinVar RCV000429502.1 Oct 12, 2018 (152)
29 ClinVar RCV001536330.2 Oct 16, 2022 (156)
30 ClinVar RCV001853243.1 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
RCV000429502.1, ss2137502343, ss2137508694 NC_000008.11:93786284:C:A NC_000008.11:93786284:C:A (self)
ss217407529 NC_000008.9:94867688:C:T NC_000008.11:93786284:C:T (self)
43153415, 9358148, 6420083, ss335057951, ss490967416, ss1330988476, ss1689252901, ss2737247537, ss3022864395, ss3653409452, ss3768333465, ss5382968509 NC_000008.10:94798512:C:T NC_000008.11:93786284:C:T (self)
RCV000201701.3, RCV001536330.2, RCV001853243.1, 56564188, 304375425, 66228326, 633512194, 3723539110, ss3726554850, ss4189384170, ss4796134634, ss5569038253, ss5732391222, ss5890098127 NC_000008.11:93786284:C:T NC_000008.11:93786284: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.

1 citation for rs116647652
PMID Title Author Year Journal
26092869 Joubert syndrome: a model for untangling recessive disorders with extreme genetic heterogeneity. Bachmann-Gagescu R et al. 2015 Journal of medical genetics
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