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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.

rs114342808

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:197421404 (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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000019 (5/264690, TOPMED)
T=0.000032 (8/251406, GnomAD_exome)
T=0.000014 (2/140224, GnomAD) (+ 7 more)
T=0.000049 (6/121406, ExAC)
T=0.000068 (7/102716, ALFA)
T=0.00006 (5/78698, PAGE_STUDY)
T=0.00021 (6/28256, 14KJPN)
T=0.00018 (3/16760, 8.3KJPN)
T=0.0007 (2/2922, KOREAN)
T=0.0016 (3/1832, Korea1K)
Clinical Significance
Reported in ClinVar
Gene : Consequence
CRB1 : Stop Gained
Publications
0 citations
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 102716 C=0.999932 T=0.000068
European Sub 89970 C=0.99994 T=0.00006
African Sub 3752 C=0.9997 T=0.0003
African Others Sub 146 C=1.000 T=0.000
African American Sub 3606 C=0.9997 T=0.0003
Asian Sub 3356 C=0.9997 T=0.0003
East Asian Sub 2704 C=0.9996 T=0.0004
Other Asian Sub 652 C=1.000 T=0.000
Latin American 1 Sub 434 C=1.000 T=0.000
Latin American 2 Sub 928 C=1.000 T=0.000
South Asian Sub 274 C=1.000 T=0.000
Other Sub 4002 C=1.0000 T=0.0000


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=0.999981 T=0.000019
gnomAD - Exomes Global Study-wide 251406 C=0.999968 T=0.000032
gnomAD - Exomes European Sub 135340 C=0.999970 T=0.000030
gnomAD - Exomes Asian Sub 49010 C=0.99994 T=0.00006
gnomAD - Exomes American Sub 34588 C=1.00000 T=0.00000
gnomAD - Exomes African Sub 16256 C=1.00000 T=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10076 C=0.99990 T=0.00010
gnomAD - Exomes Other Sub 6136 C=1.0000 T=0.0000
gnomAD - Genomes Global Study-wide 140224 C=0.999986 T=0.000014
gnomAD - Genomes European Sub 75942 C=0.99997 T=0.00003
gnomAD - Genomes African Sub 42028 C=1.00000 T=0.00000
gnomAD - Genomes American Sub 13654 C=1.00000 T=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3320 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3134 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2146 C=1.0000 T=0.0000
ExAC Global Study-wide 121406 C=0.999951 T=0.000049
ExAC Europe Sub 73350 C=0.99996 T=0.00004
ExAC Asian Sub 25166 C=0.99988 T=0.00012
ExAC American Sub 11576 C=1.00000 T=0.00000
ExAC African Sub 10406 C=1.00000 T=0.00000
ExAC Other Sub 908 C=1.000 T=0.000
Allele Frequency Aggregator Total Global 102716 C=0.999932 T=0.000068
Allele Frequency Aggregator European Sub 89970 C=0.99994 T=0.00006
Allele Frequency Aggregator Other Sub 4002 C=1.0000 T=0.0000
Allele Frequency Aggregator African Sub 3752 C=0.9997 T=0.0003
Allele Frequency Aggregator Asian Sub 3356 C=0.9997 T=0.0003
Allele Frequency Aggregator Latin American 2 Sub 928 C=1.000 T=0.000
Allele Frequency Aggregator Latin American 1 Sub 434 C=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 274 C=1.000 T=0.000
The PAGE Study Global Study-wide 78698 C=0.99994 T=0.00006
The PAGE Study AfricanAmerican Sub 32512 C=1.00000 T=0.00000
The PAGE Study Mexican Sub 10810 C=1.00000 T=0.00000
The PAGE Study Asian Sub 8318 C=0.9998 T=0.0002
The PAGE Study PuertoRican Sub 7918 C=1.0000 T=0.0000
The PAGE Study NativeHawaiian Sub 4534 C=0.9998 T=0.0002
The PAGE Study Cuban Sub 4230 C=0.9995 T=0.0005
The PAGE Study Dominican Sub 3828 C=1.0000 T=0.0000
The PAGE Study CentralAmerican Sub 2450 C=1.0000 T=0.0000
The PAGE Study SouthAmerican Sub 1982 C=1.0000 T=0.0000
The PAGE Study NativeAmerican Sub 1260 C=1.0000 T=0.0000
The PAGE Study SouthAsian Sub 856 C=1.000 T=0.000
14KJPN JAPANESE Study-wide 28256 C=0.99979 T=0.00021
8.3KJPN JAPANESE Study-wide 16760 C=0.99982 T=0.00018
KOREAN population from KRGDB KOREAN Study-wide 2922 C=0.9993 T=0.0007
Korean Genome Project KOREAN Study-wide 1832 C=0.9984 T=0.0016
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 1 NC_000001.11:g.197421404C>T
GRCh37.p13 chr 1 NC_000001.10:g.197390534C>T
CRB1 RefSeqGene NG_008483.2:g.224943C>T
Gene: CRB1, crumbs cell polarity complex component 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
CRB1 transcript variant 1 NM_201253.3:c.1576C>T R [CGA] > * [TGA] Coding Sequence Variant
protein crumbs homolog 1 isoform 1 precursor NP_957705.1:p.Arg526Ter R (Arg) > * (Ter) Stop Gained
CRB1 transcript variant 2 NM_001193640.2:c.1240C>T R [CGA] > * [TGA] Coding Sequence Variant
protein crumbs homolog 1 isoform 2 precursor NP_001180569.1:p.Arg414Ter R (Arg) > * (Ter) Stop Gained
CRB1 transcript variant 3 NM_001257965.2:c.1369C>T R [CGA] > * [TGA] Coding Sequence Variant
protein crumbs homolog 1 isoform 3 NP_001244894.1:p.Arg457Ter R (Arg) > * (Ter) Stop Gained
CRB1 transcript variant 4 NM_001257966.2:c.1576C>T R [CGA] > * [TGA] Coding Sequence Variant
protein crumbs homolog 1 isoform 4 precursor NP_001244895.1:p.Arg526Ter R (Arg) > * (Ter) Stop Gained
CRB1 transcript variant 6 NR_047564.2:n.1737C>T N/A Non Coding Transcript Variant
CRB1 transcript variant 5 NR_047563.2:n.1737C>T N/A Non Coding Transcript Variant
CRB1 transcript variant X1 XM_011509365.3:c.1576C>T R [CGA] > * [TGA] Coding Sequence Variant
protein crumbs homolog 1 isoform X1 XP_011507667.1:p.Arg526Ter R (Arg) > * (Ter) Stop Gained
CRB1 transcript variant X2 XM_047416572.1:c.1369C>T R [CGA] > * [TGA] Coding Sequence Variant
protein crumbs homolog 1 isoform X2 XP_047272528.1:p.Arg457Ter R (Arg) > * (Ter) Stop Gained
CRB1 transcript variant X3 XM_047416573.1:c.1369C>T R [CGA] > * [TGA] Coding Sequence Variant
protein crumbs homolog 1 isoform X2 XP_047272529.1:p.Arg457Ter R (Arg) > * (Ter) Stop Gained
CRB1 transcript variant X4 XM_011509367.2:c.1576C>T R [CGA] > * [TGA] Coding Sequence Variant
protein crumbs homolog 1 isoform X3 XP_011507669.1:p.Arg526Ter R (Arg) > * (Ter) Stop Gained
CRB1 transcript variant X5 XM_047416574.1:c.1240C>T R [CGA] > * [TGA] Coding Sequence Variant
protein crumbs homolog 1 isoform X4 XP_047272530.1:p.Arg414Ter R (Arg) > * (Ter) Stop Gained
CRB1 transcript variant X6 XM_047416575.1:c.715C>T R [CGA] > * [TGA] Coding Sequence Variant
protein crumbs homolog 1 isoform X5 XP_047272531.1:p.Arg239Ter R (Arg) > * (Ter) Stop Gained
CRB1 transcript variant X7 XM_011509369.3:c.19C>T R [CGA] > * [TGA] Coding Sequence Variant
protein crumbs homolog 1 isoform X6 XP_011507671.1:p.Arg7Ter R (Arg) > * (Ter) Stop Gained
CRB1 transcript variant X8 XM_017000852.2:c.1576C>T R [CGA] > * [TGA] Coding Sequence Variant
protein crumbs homolog 1 isoform X7 XP_016856341.1:p.Arg526Ter R (Arg) > * (Ter) Stop Gained
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: T (allele ID: 152885 )
ClinVar Accession Disease Names Clinical Significance
RCV000132698.4 Leber congenital amaurosis 8 Pathogenic
RCV000179572.4 not provided Pathogenic
RCV000792250.2 Leber congenital amaurosis 8,Retinitis pigmentosa 12 Pathogenic
RCV001002990.2 Leber congenital amaurosis Pathogenic
RCV001073589.1 Retinal dystrophy Pathogenic
RCV001262102.1 Leber congenital amaurosis 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= T
GRCh38.p14 chr 1 NC_000001.11:g.197421404= NC_000001.11:g.197421404C>T
GRCh37.p13 chr 1 NC_000001.10:g.197390534= NC_000001.10:g.197390534C>T
CRB1 RefSeqGene NG_008483.2:g.224943= NG_008483.2:g.224943C>T
CRB1 transcript variant 1 NM_201253.3:c.1576= NM_201253.3:c.1576C>T
CRB1 transcript variant 1 NM_201253.2:c.1576= NM_201253.2:c.1576C>T
CRB1 transcript variant 6 NR_047564.2:n.1737= NR_047564.2:n.1737C>T
CRB1 transcript variant 6 NR_047564.1:n.1785= NR_047564.1:n.1785C>T
CRB1 transcript variant 3 NM_001257965.2:c.1369= NM_001257965.2:c.1369C>T
CRB1 transcript variant 3 NM_001257965.1:c.1369= NM_001257965.1:c.1369C>T
CRB1 transcript variant 5 NR_047563.2:n.1737= NR_047563.2:n.1737C>T
CRB1 transcript variant 5 NR_047563.1:n.1785= NR_047563.1:n.1785C>T
CRB1 transcript variant 2 NM_001193640.2:c.1240= NM_001193640.2:c.1240C>T
CRB1 transcript variant 2 NM_001193640.1:c.1240= NM_001193640.1:c.1240C>T
CRB1 transcript variant 4 NM_001257966.2:c.1576= NM_001257966.2:c.1576C>T
CRB1 transcript variant 4 NM_001257966.1:c.1576= NM_001257966.1:c.1576C>T
CRB1 transcript variant X1 XM_011509365.3:c.1576= XM_011509365.3:c.1576C>T
CRB1 transcript variant X1 XM_011509365.2:c.1576= XM_011509365.2:c.1576C>T
CRB1 transcript variant X1 XM_011509365.1:c.1576= XM_011509365.1:c.1576C>T
CRB1 transcript variant X7 XM_011509369.3:c.19= XM_011509369.3:c.19C>T
CRB1 transcript variant X4 XM_011509369.2:c.19= XM_011509369.2:c.19C>T
CRB1 transcript variant X5 XM_011509369.1:c.19= XM_011509369.1:c.19C>T
CRB1 transcript variant X8 XM_017000852.2:c.1576= XM_017000852.2:c.1576C>T
CRB1 transcript variant X5 XM_017000852.1:c.1576= XM_017000852.1:c.1576C>T
CRB1 transcript variant X4 XM_011509367.2:c.1576= XM_011509367.2:c.1576C>T
CRB1 transcript variant X2 XM_011509367.1:c.1576= XM_011509367.1:c.1576C>T
CRB1 transcript variant 1 NM_012076.2:c.1576= NM_012076.2:c.1576C>T
CRB1 transcript variant X2 XM_047416572.1:c.1369= XM_047416572.1:c.1369C>T
CRB1 transcript variant X3 XM_047416573.1:c.1369= XM_047416573.1:c.1369C>T
CRB1 transcript variant X5 XM_047416574.1:c.1240= XM_047416574.1:c.1240C>T
CRB1 transcript variant X6 XM_047416575.1:c.715= XM_047416575.1:c.715C>T
CRB1 transcript NM_012076.1:c.1576= NM_012076.1:c.1576C>T
protein crumbs homolog 1 isoform 1 precursor NP_957705.1:p.Arg526= NP_957705.1:p.Arg526Ter
protein crumbs homolog 1 isoform 3 NP_001244894.1:p.Arg457= NP_001244894.1:p.Arg457Ter
protein crumbs homolog 1 isoform 2 precursor NP_001180569.1:p.Arg414= NP_001180569.1:p.Arg414Ter
protein crumbs homolog 1 isoform 4 precursor NP_001244895.1:p.Arg526= NP_001244895.1:p.Arg526Ter
protein crumbs homolog 1 isoform X1 XP_011507667.1:p.Arg526= XP_011507667.1:p.Arg526Ter
protein crumbs homolog 1 isoform X6 XP_011507671.1:p.Arg7= XP_011507671.1:p.Arg7Ter
protein crumbs homolog 1 isoform X7 XP_016856341.1:p.Arg526= XP_016856341.1:p.Arg526Ter
protein crumbs homolog 1 isoform X3 XP_011507669.1:p.Arg526= XP_011507669.1:p.Arg526Ter
protein crumbs homolog 1 isoform X2 XP_047272528.1:p.Arg457= XP_047272528.1:p.Arg457Ter
protein crumbs homolog 1 isoform X2 XP_047272529.1:p.Arg457= XP_047272529.1:p.Arg457Ter
protein crumbs homolog 1 isoform X4 XP_047272530.1:p.Arg414= XP_047272530.1:p.Arg414Ter
protein crumbs homolog 1 isoform X5 XP_047272531.1:p.Arg239= XP_047272531.1:p.Arg239Ter
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#.

23 SubSNP, 10 Frequency, 6 ClinVar submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss217393161 Jul 14, 2010 (132)
2 KYOTOUNIVOPHTHALMOL ss1226512821 Aug 11, 2014 (141)
3 EVA_EXAC ss1685975809 Apr 01, 2015 (144)
4 ILLUMINA ss1946018920 Feb 12, 2016 (147)
5 ILLUMINA ss1958344316 Feb 12, 2016 (147)
6 GNOMAD ss2732153136 Nov 08, 2017 (151)
7 GNOMAD ss2746525881 Nov 08, 2017 (151)
8 GNOMAD ss2764713047 Nov 08, 2017 (151)
9 ILLUMINA ss3021165870 Nov 08, 2017 (151)
10 ILLUMINA ss3625557995 Oct 11, 2018 (152)
11 ILLUMINA ss3644514910 Oct 11, 2018 (152)
12 ILLUMINA ss3651506450 Oct 11, 2018 (152)
13 ILLUMINA ss3725092712 Jul 12, 2019 (153)
14 EVA ss3747170741 Jul 12, 2019 (153)
15 PAGE_CC ss3770861913 Jul 12, 2019 (153)
16 KRGDB ss3895903049 Apr 25, 2020 (154)
17 KOGIC ss3946224314 Apr 25, 2020 (154)
18 TOPMED ss4478900580 Apr 25, 2021 (155)
19 TOMMO_GENOMICS ss5147827105 Apr 25, 2021 (155)
20 TOMMO_GENOMICS ss5675409233 Oct 13, 2022 (156)
21 EVA ss5847568069 Oct 13, 2022 (156)
22 EVA ss5939009524 Oct 13, 2022 (156)
23 EVA ss5979299738 Oct 13, 2022 (156)
24 ExAC NC_000001.10 - 197390534 Oct 11, 2018 (152)
25 gnomAD - Genomes NC_000001.11 - 197421404 Apr 25, 2021 (155)
26 gnomAD - Exomes NC_000001.10 - 197390534 Jul 12, 2019 (153)
27 KOREAN population from KRGDB NC_000001.10 - 197390534 Apr 25, 2020 (154)
28 Korean Genome Project NC_000001.11 - 197421404 Apr 25, 2020 (154)
29 The PAGE Study NC_000001.11 - 197421404 Jul 12, 2019 (153)
30 8.3KJPN NC_000001.10 - 197390534 Apr 25, 2021 (155)
31 14KJPN NC_000001.11 - 197421404 Oct 13, 2022 (156)
32 TopMed NC_000001.11 - 197421404 Apr 25, 2021 (155)
33 ALFA NC_000001.11 - 197421404 Apr 25, 2021 (155)
34 ClinVar RCV000132698.4 Apr 25, 2020 (154)
35 ClinVar RCV000179572.4 Oct 13, 2022 (156)
36 ClinVar RCV000792250.2 Oct 13, 2022 (156)
37 ClinVar RCV001002990.2 Oct 13, 2022 (156)
38 ClinVar RCV001073589.1 Apr 25, 2021 (155)
39 ClinVar RCV001262102.1 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss217393161 NC_000001.9:195657156:C:T NC_000001.11:197421403:C:T (self)
5206922, 1185444, 3080443, 5796412, ss1685975809, ss1946018920, ss1958344316, ss2732153136, ss2746525881, ss2764713047, ss3021165870, ss3625557995, ss3644514910, ss3651506450, ss3747170741, ss3895903049, ss5147827105, ss5847568069, ss5939009524, ss5979299738 NC_000001.10:197390533:C:T NC_000001.11:197421403:C:T (self)
RCV000132698.4, RCV000179572.4, RCV000792250.2, RCV001002990.2, RCV001073589.1, RCV001262102.1, 35729289, 2602315, 83382, 9246337, 42506915, 12443567933, ss1226512821, ss3725092712, ss3770861913, ss3946224314, ss4478900580, ss5675409233 NC_000001.11:197421403:C:T NC_000001.11:197421403: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.

No publications for rs114342808

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