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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.

rs1473598056

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr4:55443835 (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
T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.000004 (1/251122, GnomAD_exome)
C=0.000021 (3/140218, GnomAD)
C=0.00000 (0/10680, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CLOCK : Missense Variant
TMEM165 : Intron Variant
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: 20231103111315
Population Group Sample Size Ref Allele Alt Allele Ref HMOZ Alt HMOZ HTRZ HWEP
Total Global 10680 T=1.00000 C=0.00000 1.0 0.0 0.0 N/A
European Sub 6962 T=1.0000 C=0.0000 1.0 0.0 0.0 N/A
African Sub 2294 T=1.0000 C=0.0000 1.0 0.0 0.0 N/A
African Others Sub 84 T=1.00 C=0.00 1.0 0.0 0.0 N/A
African American Sub 2210 T=1.0000 C=0.0000 1.0 0.0 0.0 N/A
Asian Sub 108 T=1.000 C=0.000 1.0 0.0 0.0 N/A
East Asian Sub 84 T=1.00 C=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 24 T=1.00 C=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 T=1.000 C=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 T=1.000 C=0.000 1.0 0.0 0.0 N/A
South Asian Sub 94 T=1.00 C=0.00 1.0 0.0 0.0 N/A
Other Sub 466 T=1.000 C=0.000 1.0 0.0 0.0 N/A


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 251122 T=0.999996 C=0.000004
gnomAD - Exomes European Sub 135136 T=1.000000 C=0.000000
gnomAD - Exomes Asian Sub 48978 T=1.00000 C=0.00000
gnomAD - Exomes American Sub 34548 T=0.99997 C=0.00003
gnomAD - Exomes African Sub 16256 T=1.00000 C=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10078 T=1.00000 C=0.00000
gnomAD - Exomes Other Sub 6126 T=1.0000 C=0.0000
gnomAD - Genomes Global Study-wide 140218 T=0.999979 C=0.000021
gnomAD - Genomes European Sub 75938 T=1.00000 C=0.00000
gnomAD - Genomes African Sub 42028 T=1.00000 C=0.00000
gnomAD - Genomes American Sub 13642 T=0.99978 C=0.00022
gnomAD - Genomes Ashkenazi Jewish Sub 3324 T=1.0000 C=0.0000
gnomAD - Genomes East Asian Sub 3132 T=1.0000 C=0.0000
gnomAD - Genomes Other Sub 2154 T=1.0000 C=0.0000
Allele Frequency Aggregator Total Global 10680 T=1.00000 C=0.00000
Allele Frequency Aggregator European Sub 6962 T=1.0000 C=0.0000
Allele Frequency Aggregator African Sub 2294 T=1.0000 C=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 T=1.000 C=0.000
Allele Frequency Aggregator Other Sub 466 T=1.000 C=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 T=1.000 C=0.000
Allele Frequency Aggregator Asian Sub 108 T=1.000 C=0.000
Allele Frequency Aggregator South Asian Sub 94 T=1.00 C=0.00
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 4 NC_000004.12:g.55443835T>C
GRCh37.p13 chr 4 NC_000004.11:g.56310002T>C
Gene: TMEM165, transmembrane protein 165 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
TMEM165 transcript variant 1 NM_018475.5:c. N/A Genic Downstream Transcript Variant
TMEM165 transcript variant 2 NR_073070.2:n. N/A Genic Downstream Transcript Variant
TMEM165 transcript variant X1 XM_011534394.4:c.899-8404…

XM_011534394.4:c.899-8404T>C

 		N/A Intron Variant
TMEM165 transcript variant X2 XM_017008412.2:c. N/A Genic Downstream Transcript Variant
TMEM165 transcript variant X3 XM_047415962.1:c. N/A Genic Downstream Transcript Variant
Gene: CLOCK, clock circadian regulator (minus strand)
Molecule type Change Amino acid[Codon] SO Term
CLOCK transcript variant 2 NM_004898.4:c.1754A>G N [AAT] > S [AGT] Coding Sequence Variant
circadian locomoter output cycles protein kaput NP_004889.1:p.Asn585Ser N (Asn) > S (Ser) Missense Variant
CLOCK transcript variant 1 NM_001267843.2:c.1754A>G N [AAT] > S [AGT] Coding Sequence Variant
circadian locomoter output cycles protein kaput NP_001254772.1:p.Asn585Ser N (Asn) > S (Ser) Missense Variant
CLOCK transcript variant X1 XM_005265787.3:c.1754A>G N [AAT] > S [AGT] Coding Sequence Variant
circadian locomoter output cycles protein kaput isoform X1 XP_005265844.1:p.Asn585Ser N (Asn) > S (Ser) Missense Variant
CLOCK transcript variant X2 XM_047416431.1:c.1754A>G N [AAT] > S [AGT] Coding Sequence Variant
circadian locomoter output cycles protein kaput isoform X1 XP_047272387.1:p.Asn585Ser N (Asn) > S (Ser) Missense Variant
CLOCK transcript variant X3 XM_017008854.2:c.1754A>G N [AAT] > S [AGT] Coding Sequence Variant
circadian locomoter output cycles protein kaput isoform X1 XP_016864343.1:p.Asn585Ser N (Asn) > S (Ser) Missense Variant
CLOCK transcript variant X4 XM_011534410.3:c.1754A>G N [AAT] > S [AGT] Coding Sequence Variant
circadian locomoter output cycles protein kaput isoform X1 XP_011532712.1:p.Asn585Ser N (Asn) > S (Ser) Missense Variant
CLOCK transcript variant X5 XM_011534411.3:c.1754A>G N [AAT] > S [AGT] Coding Sequence Variant
circadian locomoter output cycles protein kaput isoform X1 XP_011532713.1:p.Asn585Ser N (Asn) > S (Ser) Missense Variant
CLOCK transcript variant X6 XM_047416432.1:c.1754A>G N [AAT] > S [AGT] Coding Sequence Variant
circadian locomoter output cycles protein kaput isoform X1 XP_047272388.1:p.Asn585Ser N (Asn) > S (Ser) Missense Variant
CLOCK transcript variant X7 XM_024454284.2:c.1754A>G N [AAT] > S [AGT] Coding Sequence Variant
circadian locomoter output cycles protein kaput isoform X1 XP_024310052.1:p.Asn585Ser N (Asn) > S (Ser) Missense Variant
CLOCK transcript variant X8 XM_047416433.1:c.1754A>G N [AAT] > S [AGT] Coding Sequence Variant
circadian locomoter output cycles protein kaput isoform X1 XP_047272389.1:p.Asn585Ser N (Asn) > S (Ser) Missense Variant
CLOCK transcript variant X9 XM_047416434.1:c.1754A>G N [AAT] > S [AGT] Coding Sequence Variant
circadian locomoter output cycles protein kaput isoform X1 XP_047272390.1:p.Asn585Ser N (Asn) > S (Ser) Missense Variant
CLOCK transcript variant X10 XM_047416435.1:c.1754A>G N [AAT] > S [AGT] Coding Sequence Variant
circadian locomoter output cycles protein kaput isoform X1 XP_047272391.1:p.Asn585Ser N (Asn) > S (Ser) Missense Variant
CLOCK transcript variant X11 XM_047416436.1:c.1754A>G N [AAT] > S [AGT] Coding Sequence Variant
circadian locomoter output cycles protein kaput isoform X1 XP_047272392.1:p.Asn585Ser N (Asn) > S (Ser) Missense Variant
CLOCK transcript variant X12 XM_047416437.1:c.1754A>G N [AAT] > S [AGT] Coding Sequence Variant
circadian locomoter output cycles protein kaput isoform X1 XP_047272393.1:p.Asn585Ser N (Asn) > S (Ser) Missense Variant
CLOCK transcript variant X13 XM_047416438.1:c.1754A>G N [AAT] > S [AGT] Coding Sequence Variant
circadian locomoter output cycles protein kaput isoform X1 XP_047272394.1:p.Asn585Ser N (Asn) > S (Ser) Missense Variant
CLOCK transcript variant X14 XM_047416439.1:c.1754A>G N [AAT] > S [AGT] Coding Sequence Variant
circadian locomoter output cycles protein kaput isoform X1 XP_047272395.1:p.Asn585Ser N (Asn) > S (Ser) Missense Variant
CLOCK transcript variant X15 XM_047416440.1:c.1754A>G N [AAT] > S [AGT] Coding Sequence Variant
circadian locomoter output cycles protein kaput isoform X1 XP_047272396.1:p.Asn585Ser N (Asn) > S (Ser) 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.

Not Reported in ClinVar
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.p14 chr 4 NC_000004.12:g.55443835= NC_000004.12:g.55443835T>C
GRCh37.p13 chr 4 NC_000004.11:g.56310002= NC_000004.11:g.56310002T>C
CLOCK transcript variant 2 NM_004898.4:c.1754= NM_004898.4:c.1754A>G
CLOCK transcript variant 2 NM_004898.3:c.1754= NM_004898.3:c.1754A>G
CLOCK transcript variant X1 XM_005265787.3:c.1754= XM_005265787.3:c.1754A>G
CLOCK transcript variant X1 XM_005265787.2:c.1754= XM_005265787.2:c.1754A>G
CLOCK transcript variant X1 XM_005265787.1:c.1754= XM_005265787.1:c.1754A>G
CLOCK transcript variant X5 XM_011534411.3:c.1754= XM_011534411.3:c.1754A>G
CLOCK transcript variant X6 XM_011534411.2:c.1754= XM_011534411.2:c.1754A>G
CLOCK transcript variant X5 XM_011534411.1:c.1754= XM_011534411.1:c.1754A>G
CLOCK transcript variant X4 XM_011534410.3:c.1754= XM_011534410.3:c.1754A>G
CLOCK transcript variant X5 XM_011534410.2:c.1754= XM_011534410.2:c.1754A>G
CLOCK transcript variant X4 XM_011534410.1:c.1754= XM_011534410.1:c.1754A>G
CLOCK transcript variant 1 NM_001267843.2:c.1754= NM_001267843.2:c.1754A>G
CLOCK transcript variant 1 NM_001267843.1:c.1754= NM_001267843.1:c.1754A>G
CLOCK transcript variant X7 XM_024454284.2:c.1754= XM_024454284.2:c.1754A>G
CLOCK transcript variant X3 XM_024454284.1:c.1754= XM_024454284.1:c.1754A>G
CLOCK transcript variant X3 XM_017008854.2:c.1754= XM_017008854.2:c.1754A>G
CLOCK transcript variant X4 XM_017008854.1:c.1754= XM_017008854.1:c.1754A>G
CLOCK transcript variant X9 XM_047416434.1:c.1754= XM_047416434.1:c.1754A>G
CLOCK transcript variant X8 XM_047416433.1:c.1754= XM_047416433.1:c.1754A>G
CLOCK transcript variant X12 XM_047416437.1:c.1754= XM_047416437.1:c.1754A>G
CLOCK transcript variant X11 XM_047416436.1:c.1754= XM_047416436.1:c.1754A>G
CLOCK transcript variant X13 XM_047416438.1:c.1754= XM_047416438.1:c.1754A>G
CLOCK transcript variant X2 XM_047416431.1:c.1754= XM_047416431.1:c.1754A>G
CLOCK transcript variant X10 XM_047416435.1:c.1754= XM_047416435.1:c.1754A>G
CLOCK transcript variant X14 XM_047416439.1:c.1754= XM_047416439.1:c.1754A>G
CLOCK transcript variant X6 XM_047416432.1:c.1754= XM_047416432.1:c.1754A>G
CLOCK transcript variant X15 XM_047416440.1:c.1754= XM_047416440.1:c.1754A>G
circadian locomoter output cycles protein kaput NP_004889.1:p.Asn585= NP_004889.1:p.Asn585Ser
circadian locomoter output cycles protein kaput isoform X1 XP_005265844.1:p.Asn585= XP_005265844.1:p.Asn585Ser
circadian locomoter output cycles protein kaput isoform X1 XP_011532713.1:p.Asn585= XP_011532713.1:p.Asn585Ser
circadian locomoter output cycles protein kaput isoform X1 XP_011532712.1:p.Asn585= XP_011532712.1:p.Asn585Ser
circadian locomoter output cycles protein kaput NP_001254772.1:p.Asn585= NP_001254772.1:p.Asn585Ser
circadian locomoter output cycles protein kaput isoform X1 XP_024310052.1:p.Asn585= XP_024310052.1:p.Asn585Ser
circadian locomoter output cycles protein kaput isoform X1 XP_016864343.1:p.Asn585= XP_016864343.1:p.Asn585Ser
circadian locomoter output cycles protein kaput isoform X1 XP_047272390.1:p.Asn585= XP_047272390.1:p.Asn585Ser
circadian locomoter output cycles protein kaput isoform X1 XP_047272389.1:p.Asn585= XP_047272389.1:p.Asn585Ser
circadian locomoter output cycles protein kaput isoform X1 XP_047272393.1:p.Asn585= XP_047272393.1:p.Asn585Ser
circadian locomoter output cycles protein kaput isoform X1 XP_047272392.1:p.Asn585= XP_047272392.1:p.Asn585Ser
circadian locomoter output cycles protein kaput isoform X1 XP_047272394.1:p.Asn585= XP_047272394.1:p.Asn585Ser
circadian locomoter output cycles protein kaput isoform X1 XP_047272387.1:p.Asn585= XP_047272387.1:p.Asn585Ser
circadian locomoter output cycles protein kaput isoform X1 XP_047272391.1:p.Asn585= XP_047272391.1:p.Asn585Ser
circadian locomoter output cycles protein kaput isoform X1 XP_047272395.1:p.Asn585= XP_047272395.1:p.Asn585Ser
circadian locomoter output cycles protein kaput isoform X1 XP_047272388.1:p.Asn585= XP_047272388.1:p.Asn585Ser
circadian locomoter output cycles protein kaput isoform X1 XP_047272396.1:p.Asn585= XP_047272396.1:p.Asn585Ser
TMEM165 transcript variant X1 XM_011534394.4:c.899-8404= XM_011534394.4:c.899-8404T>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#.

2 SubSNP, 3 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss2734515511 Nov 08, 2017 (151)
2 GNOMAD ss4111158567 Apr 26, 2021 (155)
3 gnomAD - Genomes NC_000004.12 - 55443835 Apr 26, 2021 (155)
4 gnomAD - Exomes NC_000004.11 - 56310002 Jul 13, 2019 (153)
5 ALFA NC_000004.12 - 55443835 Apr 26, 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
3618797, ss2734515511 NC_000004.11:56310001:T:C NC_000004.12:55443834:T:C (self)
149531429, 2406244500, ss4111158567 NC_000004.12:55443834:T:C NC_000004.12:55443834: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 rs1473598056

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.post820+afb47a3d