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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.

rs398100201

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr16:57857394-57857396 (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
delCT / dupCT
Variation Type
Indel Insertion and Deletion
Frequency
delCT=0.00031 (21/67928, GnomAD)
delCT=0.00004 (1/28256, 14KJPN)
delCT=0.00006 (1/16238, 8.3KJPN) (+ 1 more)
delCT=0.00000 (0/11862, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
KIFC3 : 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 11862 TCT=1.00000 T=0.00000 1.0 0.0 0.0 N/A
European Sub 7618 TCT=1.0000 T=0.0000 1.0 0.0 0.0 N/A
African Sub 2816 TCT=1.0000 T=0.0000 1.0 0.0 0.0 N/A
African Others Sub 108 TCT=1.000 T=0.000 1.0 0.0 0.0 N/A
African American Sub 2708 TCT=1.0000 T=0.0000 1.0 0.0 0.0 N/A
Asian Sub 108 TCT=1.000 T=0.000 1.0 0.0 0.0 N/A
East Asian Sub 84 TCT=1.00 T=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 24 TCT=1.00 T=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 TCT=1.000 T=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 TCT=1.000 T=0.000 1.0 0.0 0.0 N/A
South Asian Sub 94 TCT=1.00 T=0.00 1.0 0.0 0.0 N/A
Other Sub 470 TCT=1.000 T=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 - Genomes Global Study-wide 67928 TCT=0.99969 delCT=0.00031
gnomAD - Genomes European Sub 37108 TCT=0.99989 delCT=0.00011
gnomAD - Genomes African Sub 23254 TCT=0.99953 delCT=0.00047
gnomAD - Genomes American Sub 4788 TCT=0.9990 delCT=0.0010
gnomAD - Genomes Ashkenazi Jewish Sub 1190 TCT=1.0000 delCT=0.0000
gnomAD - Genomes Other Sub 966 TCT=0.999 delCT=0.001
gnomAD - Genomes East Asian Sub 622 TCT=1.000 delCT=0.000
14KJPN JAPANESE Study-wide 28256 TCT=0.99996 delCT=0.00004
8.3KJPN JAPANESE Study-wide 16238 TCT=0.99994 delCT=0.00006
Allele Frequency Aggregator Total Global 11862 TCT=1.00000 delCT=0.00000
Allele Frequency Aggregator European Sub 7618 TCT=1.0000 delCT=0.0000
Allele Frequency Aggregator African Sub 2816 TCT=1.0000 delCT=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 TCT=1.000 delCT=0.000
Allele Frequency Aggregator Other Sub 470 TCT=1.000 delCT=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 TCT=1.000 delCT=0.000
Allele Frequency Aggregator Asian Sub 108 TCT=1.000 delCT=0.000
Allele Frequency Aggregator South Asian Sub 94 TCT=1.00 delCT=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 16 NC_000016.10:g.57857395_57857396del
GRCh38.p14 chr 16 NC_000016.10:g.57857395_57857396dup
GRCh37.p13 chr 16 NC_000016.9:g.57891299_57891300del
GRCh37.p13 chr 16 NC_000016.9:g.57891299_57891300dup
Gene: KIFC3, kinesin family member C3 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
KIFC3 transcript variant 3 NM_001130099.1:c. N/A Genic Upstream Transcript Variant
KIFC3 transcript variant 2 NM_001130100.2:c. N/A Genic Upstream Transcript Variant
KIFC3 transcript variant 4 NM_001318710.2:c. N/A Genic Upstream Transcript Variant
KIFC3 transcript variant 5 NM_001318711.2:c. N/A Genic Upstream Transcript Variant
KIFC3 transcript variant 6 NM_001318712.2:c. N/A Genic Upstream Transcript Variant
KIFC3 transcript variant 7 NM_001318713.2:c. N/A Genic Upstream Transcript Variant
KIFC3 transcript variant 8 NM_001318714.2:c. N/A Genic Upstream Transcript Variant
KIFC3 transcript variant 9 NM_001318715.2:c. N/A Genic Upstream Transcript Variant
KIFC3 transcript variant 1 NM_005550.4:c. N/A Genic Upstream Transcript Variant
KIFC3 transcript variant 10 NR_134678.2:n. N/A Genic Upstream Transcript Variant
KIFC3 transcript variant X2 XM_005255937.2:c.108+5334…

XM_005255937.2:c.108+5334_108+5335del

 		N/A Intron Variant
KIFC3 transcript variant X1 XM_006721188.2:c.108+5334…

XM_006721188.2:c.108+5334_108+5335del

 		N/A Intron Variant
KIFC3 transcript variant X9 XM_011523075.2:c.108+5334…

XM_011523075.2:c.108+5334_108+5335del

 		N/A Intron Variant
KIFC3 transcript variant X10 XM_011523076.2:c.108+5334…

XM_011523076.2:c.108+5334_108+5335del

 		N/A Intron Variant
KIFC3 transcript variant X3 XM_017023221.2:c.108+5334…

XM_017023221.2:c.108+5334_108+5335del

 		N/A Intron Variant
KIFC3 transcript variant X15 XM_047434085.1:c.108+5334…

XM_047434085.1:c.108+5334_108+5335del

 		N/A Intron Variant
KIFC3 transcript variant X11 XM_011523077.2:c. N/A Genic Upstream Transcript Variant
KIFC3 transcript variant X19 XM_011523078.2:c. N/A Genic Upstream Transcript Variant
KIFC3 transcript variant X25 XM_011523079.2:c. N/A Genic Upstream Transcript Variant
KIFC3 transcript variant X13 XM_017023224.2:c. N/A Genic Upstream Transcript Variant
KIFC3 transcript variant X17 XM_017023225.2:c. N/A Genic Upstream Transcript Variant
KIFC3 transcript variant X27 XM_024450266.2:c. N/A Genic Upstream Transcript Variant
KIFC3 transcript variant X29 XM_024450267.2:c. N/A Genic Upstream Transcript Variant
KIFC3 transcript variant X28 XM_024450268.2:c. N/A Genic Upstream Transcript Variant
KIFC3 transcript variant X4 XM_047434078.1:c. N/A Genic Upstream Transcript Variant
KIFC3 transcript variant X5 XM_047434079.1:c. N/A Genic Upstream Transcript Variant
KIFC3 transcript variant X6 XM_047434080.1:c. N/A Genic Upstream Transcript Variant
KIFC3 transcript variant X7 XM_047434081.1:c. N/A Genic Upstream Transcript Variant
KIFC3 transcript variant X8 XM_047434082.1:c. N/A Genic Upstream Transcript Variant
KIFC3 transcript variant X12 XM_047434083.1:c. N/A Genic Upstream Transcript Variant
KIFC3 transcript variant X14 XM_047434084.1:c. N/A Genic Upstream Transcript Variant
KIFC3 transcript variant X16 XM_047434086.1:c. N/A Genic Upstream Transcript Variant
KIFC3 transcript variant X18 XM_047434087.1:c. N/A Genic Upstream Transcript Variant
KIFC3 transcript variant X20 XM_047434088.1:c. N/A Genic Upstream Transcript Variant
KIFC3 transcript variant X21 XM_047434089.1:c. N/A Genic Upstream Transcript Variant
KIFC3 transcript variant X22 XM_047434090.1:c. N/A Genic Upstream Transcript Variant
KIFC3 transcript variant X23 XM_047434091.1:c. N/A Genic Upstream Transcript Variant
KIFC3 transcript variant X24 XM_047434092.1:c. N/A Genic Upstream Transcript Variant
KIFC3 transcript variant X26 XM_047434093.1:c. N/A Genic Upstream Transcript 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 TCT= delCT dupCT
GRCh38.p14 chr 16 NC_000016.10:g.57857394_57857396= NC_000016.10:g.57857395_57857396del NC_000016.10:g.57857395_57857396dup
GRCh37.p13 chr 16 NC_000016.9:g.57891298_57891300= NC_000016.9:g.57891299_57891300del NC_000016.9:g.57891299_57891300dup
KIFC3 transcript variant X4 XM_005255937.1:c.108+5335= XM_005255937.1:c.108+5334_108+5335del XM_005255937.1:c.108+5334_108+5335dup
KIFC3 transcript variant X2 XM_005255937.2:c.108+5335= XM_005255937.2:c.108+5334_108+5335del XM_005255937.2:c.108+5334_108+5335dup
KIFC3 transcript variant X2 XM_005255938.1:c.108+5335= XM_005255938.1:c.108+5334_108+5335del XM_005255938.1:c.108+5334_108+5335dup
KIFC3 transcript variant X1 XM_006721188.2:c.108+5335= XM_006721188.2:c.108+5334_108+5335del XM_006721188.2:c.108+5334_108+5335dup
KIFC3 transcript variant X9 XM_011523075.2:c.108+5335= XM_011523075.2:c.108+5334_108+5335del XM_011523075.2:c.108+5334_108+5335dup
KIFC3 transcript variant X10 XM_011523076.2:c.108+5335= XM_011523076.2:c.108+5334_108+5335del XM_011523076.2:c.108+5334_108+5335dup
KIFC3 transcript variant X3 XM_017023221.2:c.108+5335= XM_017023221.2:c.108+5334_108+5335del XM_017023221.2:c.108+5334_108+5335dup
KIFC3 transcript variant X15 XM_047434085.1:c.108+5335= XM_047434085.1:c.108+5334_108+5335del XM_047434085.1:c.108+5334_108+5335dup
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#.

7 SubSNP, 4 Frequency submissions
No Submitter Submission ID Date (Build)
1 HGSV ss81514164 Jan 10, 2018 (151)
2 GMI ss155667736 Dec 06, 2013 (138)
3 GNOMAD ss2943488450 Nov 08, 2017 (151)
4 EVA_DECODE ss3699347668 Jul 13, 2019 (153)
5 TOMMO_GENOMICS ss5219764675 Apr 26, 2021 (155)
6 HUGCELL_USP ss5494445646 Oct 16, 2022 (156)
7 TOMMO_GENOMICS ss5774830420 Oct 16, 2022 (156)
8 gnomAD - Genomes NC_000016.10 - 57857394 Apr 26, 2021 (155)
9 8.3KJPN NC_000016.9 - 57891298 Apr 26, 2021 (155)
10 14KJPN NC_000016.10 - 57857394 Oct 16, 2022 (156)
11 ALFA NC_000016.10 - 57857394 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
ss81514164 NC_000016.8:56448799:CT: NC_000016.10:57857393:TCT:T (self)
77733982, ss2943488450, ss5219764675 NC_000016.9:57891297:TC: NC_000016.10:57857393:TCT:T (self)
490785942, 108667524, ss3699347668, ss5494445646, ss5774830420 NC_000016.10:57857393:TC: NC_000016.10:57857393:TCT:T (self)
10987979727 NC_000016.10:57857393:TCT:T NC_000016.10:57857393:TCT:T (self)
ss155667736 NT_010498.15:11505499:T:CTT NC_000016.10:57857393:TCT:TCTCT (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 rs398100201

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