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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.

rs1554299354

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr6:158534455-158534459 (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
delTT / dupT / dupTT
Variation Type
Indel Insertion and Deletion
Frequency
dupTT=0.00071 (20/28256, 14KJPN)
dupTT=0.00125 (21/16756, 8.3KJPN)
delTT=0.00000 (0/11862, ALFA) (+ 2 more)
dupT=0.00000 (0/11862, ALFA)
dupTT=0.00000 (0/11862, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
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 TTTTT=1.00000 TTT=0.00000, TTTTTT=0.00000, TTTTTTT=0.00000 1.0 0.0 0.0 N/A
European Sub 7618 TTTTT=1.0000 TTT=0.0000, TTTTTT=0.0000, TTTTTTT=0.0000 1.0 0.0 0.0 N/A
African Sub 2816 TTTTT=1.0000 TTT=0.0000, TTTTTT=0.0000, TTTTTTT=0.0000 1.0 0.0 0.0 N/A
African Others Sub 108 TTTTT=1.000 TTT=0.000, TTTTTT=0.000, TTTTTTT=0.000 1.0 0.0 0.0 N/A
African American Sub 2708 TTTTT=1.0000 TTT=0.0000, TTTTTT=0.0000, TTTTTTT=0.0000 1.0 0.0 0.0 N/A
Asian Sub 108 TTTTT=1.000 TTT=0.000, TTTTTT=0.000, TTTTTTT=0.000 1.0 0.0 0.0 N/A
East Asian Sub 84 TTTTT=1.00 TTT=0.00, TTTTTT=0.00, TTTTTTT=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 24 TTTTT=1.00 TTT=0.00, TTTTTT=0.00, TTTTTTT=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 TTTTT=1.000 TTT=0.000, TTTTTT=0.000, TTTTTTT=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 TTTTT=1.000 TTT=0.000, TTTTTT=0.000, TTTTTTT=0.000 1.0 0.0 0.0 N/A
South Asian Sub 94 TTTTT=1.00 TTT=0.00, TTTTTT=0.00, TTTTTTT=0.00 1.0 0.0 0.0 N/A
Other Sub 470 TTTTT=1.000 TTT=0.000, TTTTTT=0.000, TTTTTTT=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
14KJPN JAPANESE Study-wide 28256 -

No frequency provided

dupTT=0.00071
8.3KJPN JAPANESE Study-wide 16756 -

No frequency provided

dupTT=0.00125
Allele Frequency Aggregator Total Global 11862 (T)5=1.00000 delTT=0.00000, dupT=0.00000, dupTT=0.00000
Allele Frequency Aggregator European Sub 7618 (T)5=1.0000 delTT=0.0000, dupT=0.0000, dupTT=0.0000
Allele Frequency Aggregator African Sub 2816 (T)5=1.0000 delTT=0.0000, dupT=0.0000, dupTT=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 (T)5=1.000 delTT=0.000, dupT=0.000, dupTT=0.000
Allele Frequency Aggregator Other Sub 470 (T)5=1.000 delTT=0.000, dupT=0.000, dupTT=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 (T)5=1.000 delTT=0.000, dupT=0.000, dupTT=0.000
Allele Frequency Aggregator Asian Sub 108 (T)5=1.000 delTT=0.000, dupT=0.000, dupTT=0.000
Allele Frequency Aggregator South Asian Sub 94 (T)5=1.00 delTT=0.00, dupT=0.00, dupTT=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 6 NC_000006.12:g.158534458_158534459del
GRCh38.p14 chr 6 NC_000006.12:g.158534459dup
GRCh38.p14 chr 6 NC_000006.12:g.158534458_158534459dup
GRCh37.p13 chr 6 NC_000006.11:g.158955490_158955491del
GRCh37.p13 chr 6 NC_000006.11:g.158955491dup
GRCh37.p13 chr 6 NC_000006.11:g.158955490_158955491dup
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)5= delTT dupT dupTT
GRCh38.p14 chr 6 NC_000006.12:g.158534455_158534459= NC_000006.12:g.158534458_158534459del NC_000006.12:g.158534459dup NC_000006.12:g.158534458_158534459dup
GRCh37.p13 chr 6 NC_000006.11:g.158955487_158955491= NC_000006.11:g.158955490_158955491del NC_000006.11:g.158955491dup NC_000006.11:g.158955490_158955491dup
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#.

6 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss4154963511 Apr 26, 2021 (155)
2 GNOMAD ss4154963515 Apr 26, 2021 (155)
3 GNOMAD ss4154963516 Apr 26, 2021 (155)
4 TOMMO_GENOMICS ss5180845700 Apr 26, 2021 (155)
5 HUGCELL_USP ss5468450830 Oct 14, 2022 (156)
6 TOMMO_GENOMICS ss5719992749 Oct 14, 2022 (156)
7 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 247028344 (NC_000006.12:158534454::T 1/126132)
Row 247028348 (NC_000006.12:158534454::TT 3/126132)
Row 247028349 (NC_000006.12:158534454:TT: 18/126130)

- Apr 26, 2021 (155)
8 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 247028344 (NC_000006.12:158534454::T 1/126132)
Row 247028348 (NC_000006.12:158534454::TT 3/126132)
Row 247028349 (NC_000006.12:158534454:TT: 18/126130)

- Apr 26, 2021 (155)
9 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 247028344 (NC_000006.12:158534454::T 1/126132)
Row 247028348 (NC_000006.12:158534454::TT 3/126132)
Row 247028349 (NC_000006.12:158534454:TT: 18/126130)

- Apr 26, 2021 (155)
10 8.3KJPN NC_000006.11 - 158955487 Apr 26, 2021 (155)
11 14KJPN NC_000006.12 - 158534455 Oct 14, 2022 (156)
12 ALFA NC_000006.12 - 158534455 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
ss4154963516, ss5468450830 NC_000006.12:158534454:TT: NC_000006.12:158534454:TTTTT:TTT (self)
14239869805 NC_000006.12:158534454:TTTTT:TTT NC_000006.12:158534454:TTTTT:TTT (self)
ss4154963511 NC_000006.12:158534454::T NC_000006.12:158534454:TTTTT:TTTTTT (self)
14239869805 NC_000006.12:158534454:TTTTT:TTTTTT NC_000006.12:158534454:TTTTT:TTTTTT (self)
38815007, ss5180845700 NC_000006.11:158955486::TT NC_000006.12:158534454:TTTTT:TTTTT…

NC_000006.12:158534454:TTTTT:TTTTTTT

(self)
53829853, ss4154963515, ss5719992749 NC_000006.12:158534454::TT NC_000006.12:158534454:TTTTT:TTTTT…

NC_000006.12:158534454:TTTTT:TTTTTTT

(self)
14239869805 NC_000006.12:158534454:TTTTT:TTTTT…

NC_000006.12:158534454:TTTTT:TTTTTTT

NC_000006.12:158534454:TTTTT:TTTTT…

NC_000006.12:158534454:TTTTT:TTTTTTT

(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 rs1554299354

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