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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.

rs72653091

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr2:21009626 (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>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.00056 (138/245480, GnomAD)
G=0.00214 (269/125568, TOPMED)
G=0.0023 (72/30986, GnomAD) (+ 2 more)
G=0.0015 (20/13004, GO-ESP)
G=0.003 (15/5008, 1000G)
Clinical Significance
Reported in ClinVar
Gene : Consequence
APOB : Missense 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 2 NC_000002.12:g.21009626T>A
GRCh38.p12 chr 2 NC_000002.12:g.21009626T>G
GRCh37.p13 chr 2 NC_000002.11:g.21232498T>A
GRCh37.p13 chr 2 NC_000002.11:g.21232498T>G
APOB RefSeqGene NG_011793.1:g.39448A>T
APOB RefSeqGene NG_011793.1:g.39448A>C
Gene: APOB, apolipoprotein B (minus strand)
Molecule type Change Amino acid[Codon] SO Term
APOB transcript NM_000384.2:c.7242A>T E [GAA] > D [GAT] Coding Sequence Variant
apolipoprotein B-100 precursor NP_000375.2:p.Glu2414Asp E (Glu) > D (Asp) Missense Variant
APOB transcript NM_000384.2:c.7242A>C E [GAA] > D [GAC] Coding Sequence Variant
apolipoprotein B-100 precursor NP_000375.2:p.Glu2414Asp E (Glu) > D (Asp) Missense 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: G (allele ID: 287234 )
ClinVar Accession Disease Names Clinical Significance
RCV000336043.1 Familial hypercholesterolemia Uncertain-Significance
RCV000372264.1 Familial hypobetalipoproteinemia Uncertain-Significance
RCV000655147.1 Hypercholesterolemia, autosomal dominant, type B,Hypobetalipoproteinemia, familial, 1 Benign
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
gnomAD - Exomes Global Study-wide 245480 T=0.99943 G=0.00056, A=0.00001
gnomAD - Exomes European Sub 133456 T=0.99997 G=0.00001, A=0.00001
gnomAD - Exomes Asian Sub 47970 T=1.0000 G=0.0000, A=0.0000
gnomAD - Exomes American Sub 33494 T=0.9997 G=0.0003, A=0.0000
gnomAD - Exomes African Sub 15262 T=0.9921 G=0.0079, A=0.0000
gnomAD - Exomes Ashkenazi Jewish Sub 9838 T=1.000 G=0.000, A=0.000
gnomAD - Exomes Other Sub 5460 T=0.999 G=0.001, A=0.000
TopMed Global Study-wide 125568 T=0.99786 G=0.00214
gnomAD - Genomes Global Study-wide 30986 T=0.9977 G=0.0023
gnomAD - Genomes European Sub 18508 T=1.0000 G=0.0000
gnomAD - Genomes African Sub 8736 T=0.992 G=0.008
gnomAD - Genomes East Asian Sub 1620 T=1.000 G=0.000
gnomAD - Genomes Other Sub 982 T=1.00 G=0.00
gnomAD - Genomes American Sub 838 T=1.00 G=0.00
gnomAD - Genomes Ashkenazi Jewish Sub 302 T=1.00 G=0.00
GO Exome Sequencing Project Global Study-wide 13004 T=0.9985 G=0.0015
GO Exome Sequencing Project European American Sub 8598 T=1.000 G=0.000
GO Exome Sequencing Project African American Sub 4406 T=0.995 G=0.005
1000Genomes Global Study-wide 5008 T=0.997 G=0.003
1000Genomes African Sub 1322 T=0.989 G=0.011
1000Genomes East Asian Sub 1008 T=1.000 G=0.000
1000Genomes Europe Sub 1006 T=1.000 G=0.000
1000Genomes South Asian Sub 978 T=1.00 G=0.00
1000Genomes American Sub 694 T=1.00 G=0.00
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 G Note
GRCh38.p12 chr 2 NC_000002.12:g.21...

NC_000002.12:g.21009626T=

NC_000002.12:g.21...

NC_000002.12:g.21009626T>A

NC_000002.12:g.21...

NC_000002.12:g.21009626T>G

GRCh37.p13 chr 2 NC_000002.11:g.21...

NC_000002.11:g.21232498T=

NC_000002.11:g.21...

NC_000002.11:g.21232498T>A

NC_000002.11:g.21...

NC_000002.11:g.21232498T>G

APOB RefSeqGene NG_011793.1:g.394...

NG_011793.1:g.39448A=

NG_011793.1:g.394...

NG_011793.1:g.39448A>T

NG_011793.1:g.394...

NG_011793.1:g.39448A>C

APOB transcript NM_000384.2:c.7242A= NM_000384.2:c.724...

NM_000384.2:c.7242A>T

NM_000384.2:c.724...

NM_000384.2:c.7242A>C

apolipoprotein B-100 precursor NP_000375.2:p.Glu...

NP_000375.2:p.Glu2414=

NP_000375.2:p.Glu...

NP_000375.2:p.Glu2414Asp

NP_000375.2:p.Glu...

NP_000375.2:p.Glu2414Asp

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, 7 Frequency, 3 ClinVar submissions
No Submitter Submission ID Date (Build)
1 RSG_UW ss107936402 Feb 13, 2009 (130)
2 ILLUMINA ss161072785 Dec 01, 2009 (131)
3 1000GENOMES ss210842000 Jul 14, 2010 (132)
4 1000GENOMES ss219112713 Jul 14, 2010 (132)
5 NHLBI-ESP ss342047559 May 09, 2011 (134)
6 ILLUMINA ss410831518 Sep 17, 2011 (135)
7 ILLUMINA ss479203586 Sep 08, 2015 (146)
8 ILLUMINA ss480541465 May 04, 2012 (137)
9 ILLUMINA ss484003499 May 04, 2012 (137)
10 1000GENOMES ss489805638 May 04, 2012 (137)
11 EXOME_CHIP ss491315754 May 04, 2012 (137)
12 ILLUMINA ss533802812 Sep 08, 2015 (146)
13 ILLUMINA ss778663051 Aug 21, 2014 (142)
14 ILLUMINA ss780772092 Aug 21, 2014 (142)
15 ILLUMINA ss781256689 Aug 21, 2014 (142)
16 ILLUMINA ss783451785 Aug 21, 2014 (142)
17 ILLUMINA ss834121258 Aug 21, 2014 (142)
18 1000GENOMES ss1296218047 Aug 21, 2014 (142)
19 EVA_EXAC ss1686201751 Apr 01, 2015 (144)
20 EVA_EXAC ss1686201752 Apr 01, 2015 (144)
21 EVA_MGP ss1710955662 Apr 01, 2015 (144)
22 ILLUMINA ss1752336650 Sep 08, 2015 (146)
23 ILLUMINA ss1917746409 Feb 12, 2016 (147)
24 ILLUMINA ss1946033942 Feb 12, 2016 (147)
25 ILLUMINA ss1958395781 Feb 12, 2016 (147)
26 HUMAN_LONGEVITY ss2228148564 Dec 20, 2016 (150)
27 TOPMED ss2394061672 Dec 20, 2016 (150)
28 ILLUMINA ss2633582603 Nov 08, 2017 (151)
29 GNOMAD ss2732500494 Nov 08, 2017 (151)
30 GNOMAD ss2746631518 Nov 08, 2017 (151)
31 GNOMAD ss2770587615 Nov 08, 2017 (151)
32 AFFY ss2985160957 Nov 08, 2017 (151)
33 ILLUMINA ss3021947888 Nov 08, 2017 (151)
34 TOPMED ss3301257756 Nov 08, 2017 (151)
35 ILLUMINA ss3628009208 Oct 11, 2018 (152)
36 ILLUMINA ss3628009209 Oct 11, 2018 (152)
37 ILLUMINA ss3631551389 Oct 11, 2018 (152)
38 ILLUMINA ss3634754709 Oct 11, 2018 (152)
39 ILLUMINA ss3636440918 Oct 11, 2018 (152)
40 ILLUMINA ss3640462013 Oct 11, 2018 (152)
41 ILLUMINA ss3644736634 Oct 11, 2018 (152)
42 ILLUMINA ss3652376709 Oct 11, 2018 (152)
43 ILLUMINA ss3653931547 Oct 11, 2018 (152)
44 1000Genomes NC_000002.11 - 21232498 Oct 11, 2018 (152)
45 ExAC

Submission ignored due to conflicting rows:
Row 6063819 (NC_000002.11:21232497:T:T 119955/119956, NC_000002.11:21232497:T:A 1/119956)
Row 6063820 (NC_000002.11:21232497:T:T 119874/119956, NC_000002.11:21232497:T:G 82/119956)

- Oct 11, 2018 (152)
46 ExAC

Submission ignored due to conflicting rows:
Row 6063819 (NC_000002.11:21232497:T:T 119955/119956, NC_000002.11:21232497:T:A 1/119956)
Row 6063820 (NC_000002.11:21232497:T:T 119874/119956, NC_000002.11:21232497:T:G 82/119956)

- Oct 11, 2018 (152)
47 gnomAD - Genomes NC_000002.11 - 21232498 Oct 11, 2018 (152)
48 gnomAD - Exomes NC_000002.11 - 21232498 Oct 11, 2018 (152)
49 GO Exome Sequencing Project NC_000002.11 - 21232498 Oct 11, 2018 (152)
50 TopMed NC_000002.12 - 21009626 Oct 11, 2018 (152)
51 ClinVar RCV000336043.1 Oct 11, 2018 (152)
52 ClinVar RCV000372264.1 Oct 11, 2018 (152)
53 ClinVar RCV000655147.1 Oct 11, 2018 (152)
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
ss161072785, ss210842000, ss410831518, ss484003499 NC_000002.10:21086002:T= NC_000002.12:21009625:T= (self)
7130080, 100077476, 1226245, 205438, ss219112713, ss342047559, ss479203586, ss480541465, ss489805638, ss491315754, ss533802812, ss778663051, ss780772092, ss781256689, ss783451785, ss834121258, ss1296218047, ss1686201751, ss1686201752, ss1710955662, ss1752336650, ss1917746409, ss1946033942, ss1958395781, ss2394061672, ss2633582603, ss2732500494, ss2746631518, ss2770587615, ss2985160957, ss3021947888, ss3628009208, ss3628009209, ss3631551389, ss3634754709, ss3636440918, ss3640462013, ss3644736634, ss3652376709, ss3653931547 NC_000002.11:21232497:T= NC_000002.12:21009625:T= (self)
187543813, ss2228148564, ss3301257756 NC_000002.12:21009625:T= NC_000002.12:21009625:T= (self)
ss107936402 NT_022184.15:54384:T= NC_000002.12:21009625:T= (self)
1226245, ss1686201751, ss2732500494 NC_000002.11:21232497:T>A NC_000002.12:21009625:T>A (self)
ss161072785, ss210842000, ss410831518, ss484003499 NC_000002.10:21086002:T>G NC_000002.12:21009625:T>G (self)
7130080, 100077476, 1226245, 205438, ss219112713, ss342047559, ss479203586, ss480541465, ss489805638, ss491315754, ss533802812, ss778663051, ss780772092, ss781256689, ss783451785, ss834121258, ss1296218047, ss1686201752, ss1710955662, ss1752336650, ss1917746409, ss1946033942, ss1958395781, ss2394061672, ss2633582603, ss2732500494, ss2746631518, ss2770587615, ss2985160957, ss3021947888, ss3628009208, ss3628009209, ss3631551389, ss3634754709, ss3636440918, ss3640462013, ss3644736634, ss3652376709, ss3653931547 NC_000002.11:21232497:T>G NC_000002.12:21009625:T>G (self)
RCV000336043.1, RCV000372264.1, RCV000655147.1, 187543813, ss2228148564, ss3301257756 NC_000002.12:21009625:T>G NC_000002.12:21009625:T>G (self)
ss107936402 NT_022184.15:54384:T>G NC_000002.12:21009625: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 rs72653091

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.post63+3f7b20b