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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.


Current Build 153

Released July 9, 2019

Homo sapiens
chr9:100455114 (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.

Variation Type
SNV Single Nucleotide Variation
C=0.00835 (1048/125568, TOPMED)
C=0.0072 (225/31390, GnomAD)
C=0.010 (50/5008, 1000G) (+ 4 more)
C=0.006 (28/4480, Estonian)
C=0.012 (47/3854, ALSPAC)
C=0.014 (53/3708, TWINSUK)
C=0.00 (1/600, NorthernSweden)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
MSANTD3-TMEFF1 : Intron Variant
0 citations
Genomic View
See rs on genome

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 9 NC_000009.12:g.100455114T>C
GRCh37.p13 chr 9 NC_000009.11:g.103217396T>C
Gene: MSANTD3-TMEFF1, MSANTD3-TMEFF1 readthrough (plus strand)
Molecule type Change Amino acid[Codon] SO Term
MSANTD3-TMEFF1 transcript NM_001198812.1:c. N/A Intron Variant

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

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").

Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 125568 T=0.99165 C=0.00835
gnomAD - Genomes Global Study-wide 31390 T=0.9928 C=0.0072
gnomAD - Genomes European Sub 18896 T=0.9902 C=0.0098
gnomAD - Genomes African Sub 8708 T=0.998 C=0.002
gnomAD - Genomes East Asian Sub 1560 T=0.999 C=0.001
gnomAD - Genomes Other Sub 1088 T=0.992 C=0.008
gnomAD - Genomes American Sub 848 T=0.99 C=0.01
gnomAD - Genomes Ashkenazi Jewish Sub 290 T=0.99 C=0.01
1000Genomes Global Study-wide 5008 T=0.990 C=0.010
1000Genomes African Sub 1322 T=0.999 C=0.001
1000Genomes East Asian Sub 1008 T=1.000 C=0.000
1000Genomes Europe Sub 1006 T=0.996 C=0.004
1000Genomes South Asian Sub 978 T=0.97 C=0.03
1000Genomes American Sub 694 T=0.98 C=0.02
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.994 C=0.006
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.988 C=0.012
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.986 C=0.014
Northern Sweden ACPOP Study-wide 600 T=1.00 C=0.00

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= C Note
GRCh38.p12 chr 9 NC_000009.12:g.100455114= NC_000009.12:g.10045511...


GRCh37.p13 chr 9 NC_000009.11:g.103217396= NC_000009.11:g.10321739...



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#.

19 SubSNP, 7 Frequency submissions
No Submitter Submission ID Date (Build)
1 WIAF ss1238 Sep 19, 2000 (36)
2 1000GENOMES ss335698666 May 09, 2011 (134)
3 ILLUMINA ss535154989 Sep 08, 2015 (146)
4 EVA-GONL ss986802277 Aug 21, 2014 (142)
5 1000GENOMES ss1334793837 Aug 21, 2014 (142)
6 EVA_DECODE ss1596438546 Apr 01, 2015 (144)
7 EVA_UK10K_ALSPAC ss1623206856 Apr 01, 2015 (144)
8 EVA_UK10K_TWINSUK ss1666200889 Apr 01, 2015 (144)
9 WEILL_CORNELL_DGM ss1930116188 Feb 12, 2016 (147)
10 JJLAB ss2025776274 Sep 14, 2016 (149)
11 HUMAN_LONGEVITY ss2313058819 Dec 20, 2016 (150)
12 TOPMED ss2483539538 Dec 20, 2016 (150)
13 GNOMAD ss2881346471 Nov 08, 2017 (151)
14 SWEGEN ss3005321240 Nov 08, 2017 (151)
15 TOPMED ss3596317637 Nov 08, 2017 (151)
16 ILLUMINA ss3630316062 Oct 12, 2018 (152)
17 EGCUT_WGS ss3672856323 Jul 13, 2019 (153)
18 EVA_DECODE ss3724424451 Jul 13, 2019 (153)
19 ACPOP ss3736728574 Jul 13, 2019 (153)
20 1000Genomes NC_000009.11 - 103217396 Oct 12, 2018 (152)
21 The Avon Longitudinal Study of Parents and Children NC_000009.11 - 103217396 Oct 12, 2018 (152)
22 Genetic variation in the Estonian population NC_000009.11 - 103217396 Oct 12, 2018 (152)
23 gnomAD - Genomes NC_000009.11 - 103217396 Jul 13, 2019 (153)
24 Northern Sweden NC_000009.11 - 103217396 Jul 13, 2019 (153)
25 TopMed NC_000009.12 - 100455114 Oct 12, 2018 (152)
26 UK 10K study - Twins NC_000009.11 - 103217396 Oct 12, 2018 (152)

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
ss1596438546 NC_000009.10:102257216:T:C NC_000009.12:100455113:T:C (self)
47087814, 26157422, 18594571, 128805700, 10013439, 26157422, ss335698666, ss535154989, ss986802277, ss1334793837, ss1623206856, ss1666200889, ss1930116188, ss2025776274, ss2483539538, ss2881346471, ss3005321240, ss3630316062, ss3672856323, ss3736728574 NC_000009.11:103217395:T:C NC_000009.12:100455113:T:C (self)
416607774, ss2313058819, ss3596317637, ss3724424451 NC_000009.12:100455113:T:C NC_000009.12:100455113:T:C (self)
ss1238 NT_008470.19:32381927:T:C NC_000009.12:100455113:T:C (self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs1213

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.post270+ab078da