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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.

rs10922218

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:197405408 (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
T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.338687 (89647/264690, TOPMED)
C=0.328023 (44823/136646, GnomAD)
C=0.18164 (3044/16758, 8.3KJPN) (+ 6 more)
C=0.31943 (5217/16332, ALFA)
C=0.3089 (1547/5008, 1000G)
C=0.2045 (596/2914, KOREAN)
C=0.296 (295/998, GoNL)
T=0.375 (90/240, SGDP_PRJ)
C=0.389 (84/216, Qatari)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CRB1 : 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 1 NC_000001.11:g.197405408T>C
GRCh37.p13 chr 1 NC_000001.10:g.197374538T>C
CRB1 RefSeqGene NG_008483.2:g.208947T>C
Gene: CRB1, crumbs cell polarity complex component 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
CRB1 transcript variant 2 NM_001193640.2:c.836-1559…

NM_001193640.2:c.836-15592T>C

N/A Intron Variant
CRB1 transcript variant 3 NM_001257965.2:c.965-1559…

NM_001257965.2:c.965-15592T>C

N/A Intron Variant
CRB1 transcript variant 4 NM_001257966.2:c.1172-155…

NM_001257966.2:c.1172-15592T>C

N/A Intron Variant
CRB1 transcript variant 1 NM_201253.3:c.1172-15592T…

NM_201253.3:c.1172-15592T>C

N/A Intron Variant
CRB1 transcript variant 5 NR_047563.2:n. N/A Intron Variant
CRB1 transcript variant 6 NR_047564.2:n. N/A Intron Variant
CRB1 transcript variant X1 XM_011509365.2:c.1172-155…

XM_011509365.2:c.1172-15592T>C

N/A Intron Variant
CRB1 transcript variant X2 XM_011509367.1:c.1172-155…

XM_011509367.1:c.1172-15592T>C

N/A Intron Variant
CRB1 transcript variant X4 XM_011509369.2:c.-386-155…

XM_011509369.2:c.-386-15592T>C

N/A Intron Variant
CRB1 transcript variant X3 XM_017000851.1:c.329-1559…

XM_017000851.1:c.329-15592T>C

N/A Intron Variant
CRB1 transcript variant X5 XM_017000852.1:c.1172-155…

XM_017000852.1:c.1172-15592T>C

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 16332 T=0.68057 C=0.31943
European Sub 12080 T=0.70132 C=0.29868
African Sub 2816 T=0.5714 C=0.4286
African Others Sub 108 T=0.574 C=0.426
African American Sub 2708 T=0.5713 C=0.4287
Asian Sub 108 T=0.796 C=0.204
East Asian Sub 84 T=0.77 C=0.23
Other Asian Sub 24 T=0.88 C=0.12
Latin American 1 Sub 146 T=0.630 C=0.370
Latin American 2 Sub 610 T=0.764 C=0.236
South Asian Sub 94 T=0.77 C=0.23
Other Sub 478 T=0.665 C=0.335


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 T=0.661313 C=0.338687
gnomAD - Genomes Global Study-wide 136646 T=0.671977 C=0.328023
gnomAD - Genomes European Sub 74188 T=0.70181 C=0.29819
gnomAD - Genomes African Sub 40690 T=0.58415 C=0.41585
gnomAD - Genomes American Sub 13334 T=0.72919 C=0.27081
gnomAD - Genomes Ashkenazi Jewish Sub 3274 T=0.7523 C=0.2477
gnomAD - Genomes East Asian Sub 3058 T=0.7747 C=0.2253
gnomAD - Genomes Other Sub 2102 T=0.6817 C=0.3183
8.3KJPN JAPANESE Study-wide 16758 T=0.81836 C=0.18164
Allele Frequency Aggregator Total Global 16332 T=0.68057 C=0.31943
Allele Frequency Aggregator European Sub 12080 T=0.70132 C=0.29868
Allele Frequency Aggregator African Sub 2816 T=0.5714 C=0.4286
Allele Frequency Aggregator Latin American 2 Sub 610 T=0.764 C=0.236
Allele Frequency Aggregator Other Sub 478 T=0.665 C=0.335
Allele Frequency Aggregator Latin American 1 Sub 146 T=0.630 C=0.370
Allele Frequency Aggregator Asian Sub 108 T=0.796 C=0.204
Allele Frequency Aggregator South Asian Sub 94 T=0.77 C=0.23
1000Genomes Global Study-wide 5008 T=0.6911 C=0.3089
1000Genomes African Sub 1322 T=0.5431 C=0.4569
1000Genomes East Asian Sub 1008 T=0.7708 C=0.2292
1000Genomes Europe Sub 1006 T=0.7087 C=0.2913
1000Genomes South Asian Sub 978 T=0.759 C=0.241
1000Genomes American Sub 694 T=0.736 C=0.264
KOREAN population from KRGDB KOREAN Study-wide 2914 T=0.7955 C=0.2045
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.704 C=0.296
SGDP_PRJ Global Study-wide 240 T=0.375 C=0.625
Qatari Global Study-wide 216 T=0.611 C=0.389
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= C
GRCh38.p13 chr 1 NC_000001.11:g.197405408= NC_000001.11:g.197405408T>C
GRCh37.p13 chr 1 NC_000001.10:g.197374538= NC_000001.10:g.197374538T>C
CRB1 RefSeqGene NG_008483.2:g.208947= NG_008483.2:g.208947T>C
CRB1 transcript variant 2 NM_001193640.1:c.836-15592= NM_001193640.1:c.836-15592T>C
CRB1 transcript variant 2 NM_001193640.2:c.836-15592= NM_001193640.2:c.836-15592T>C
CRB1 transcript variant 3 NM_001257965.1:c.965-15592= NM_001257965.1:c.965-15592T>C
CRB1 transcript variant 3 NM_001257965.2:c.965-15592= NM_001257965.2:c.965-15592T>C
CRB1 transcript variant 4 NM_001257966.1:c.1172-15592= NM_001257966.1:c.1172-15592T>C
CRB1 transcript variant 4 NM_001257966.2:c.1172-15592= NM_001257966.2:c.1172-15592T>C
CRB1 transcript variant 1 NM_201253.2:c.1172-15592= NM_201253.2:c.1172-15592T>C
CRB1 transcript variant 1 NM_201253.3:c.1172-15592= NM_201253.3:c.1172-15592T>C
CRB1 transcript variant X1 XM_011509365.2:c.1172-15592= XM_011509365.2:c.1172-15592T>C
CRB1 transcript variant X2 XM_011509367.1:c.1172-15592= XM_011509367.1:c.1172-15592T>C
CRB1 transcript variant X4 XM_011509369.2:c.-386-15592= XM_011509369.2:c.-386-15592T>C
CRB1 transcript variant X3 XM_017000851.1:c.329-15592= XM_017000851.1:c.329-15592T>C
CRB1 transcript variant X5 XM_017000852.1:c.1172-15592= XM_017000852.1:c.1172-15592T>C
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#.

19 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 CSHL-HAPMAP ss16384221 Feb 27, 2004 (120)
2 SC_SNP ss19058856 Feb 27, 2004 (120)
3 BCM-HGSC-SUB ss205530463 Jul 04, 2010 (142)
4 1000GENOMES ss329138300 May 09, 2011 (134)
5 SSMP ss648610159 Apr 25, 2013 (138)
6 EVA-GONL ss976000568 Aug 21, 2014 (142)
7 1000GENOMES ss1294118236 Aug 21, 2014 (142)
8 WEILL_CORNELL_DGM ss1919231841 Feb 12, 2016 (147)
9 GRF ss2698150533 Nov 08, 2017 (151)
10 GNOMAD ss2764711758 Nov 08, 2017 (151)
11 SWEGEN ss2988230179 Nov 08, 2017 (151)
12 TOPMED ss3099940392 Nov 08, 2017 (151)
13 URBANLAB ss3646857860 Oct 11, 2018 (152)
14 EVA ss3747170624 Jul 12, 2019 (153)
15 KHV_HUMAN_GENOMES ss3800177991 Jul 12, 2019 (153)
16 SGDP_PRJ ss3850623816 Apr 25, 2020 (154)
17 KRGDB ss3895902763 Apr 25, 2020 (154)
18 TOPMED ss4478896505 Apr 25, 2021 (155)
19 TOMMO_GENOMICS ss5147826570 Apr 25, 2021 (155)
20 1000Genomes NC_000001.10 - 197374538 Oct 11, 2018 (152)
21 gnomAD - Genomes NC_000001.11 - 197405408 Apr 25, 2021 (155)
22 Genome of the Netherlands Release 5 NC_000001.10 - 197374538 Apr 25, 2020 (154)
23 KOREAN population from KRGDB NC_000001.10 - 197374538 Apr 25, 2020 (154)
24 Qatari NC_000001.10 - 197374538 Apr 25, 2020 (154)
25 SGDP_PRJ NC_000001.10 - 197374538 Apr 25, 2020 (154)
26 8.3KJPN NC_000001.10 - 197374538 Apr 25, 2021 (155)
27 TopMed NC_000001.11 - 197405408 Apr 25, 2021 (155)
28 ALFA NC_000001.11 - 197405408 Apr 25, 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)
rs113472322 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss205530463 NC_000001.9:195641160:T:C NC_000001.11:197405407:T:C (self)
4953543, 1187724, 3080157, 1273771, 2640796, 5795877, ss329138300, ss648610159, ss976000568, ss1294118236, ss1919231841, ss2698150533, ss2764711758, ss2988230179, ss3747170624, ss3850623816, ss3895902763, ss5147826570 NC_000001.10:197374537:T:C NC_000001.11:197405407:T:C (self)
35725924, 42502840, 1881379161, ss3099940392, ss3646857860, ss3800177991, ss4478896505 NC_000001.11:197405407:T:C NC_000001.11:197405407:T:C (self)
ss19058856 NT_004487.19:48863179:T:C NC_000001.11:197405407:T:C (self)
ss16384221 NT_004671.15:8729523:T:C NC_000001.11:197405407:T:C (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 rs10922218

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