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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.

rs1204737305

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr17:40966058-40966066 (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
delGTGT / dupGT / dupGTGT
Variation Type
Indel Insertion and Deletion
Frequency
delGTGT=0.00000 (0/11856, ALFA)
dupGT=0.00000 (0/11856, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
KRT39 : Intron Variant
LOC107985072 : 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 11856 TGTGTGTGT=1.00000 TGTGT=0.00000, TGTGTGTGTGT=0.00000 1.0 0.0 0.0 N/A
European Sub 7618 TGTGTGTGT=1.0000 TGTGT=0.0000, TGTGTGTGTGT=0.0000 1.0 0.0 0.0 N/A
African Sub 2810 TGTGTGTGT=1.0000 TGTGT=0.0000, TGTGTGTGTGT=0.0000 1.0 0.0 0.0 N/A
African Others Sub 108 TGTGTGTGT=1.000 TGTGT=0.000, TGTGTGTGTGT=0.000 1.0 0.0 0.0 N/A
African American Sub 2702 TGTGTGTGT=1.0000 TGTGT=0.0000, TGTGTGTGTGT=0.0000 1.0 0.0 0.0 N/A
Asian Sub 108 TGTGTGTGT=1.000 TGTGT=0.000, TGTGTGTGTGT=0.000 1.0 0.0 0.0 N/A
East Asian Sub 84 TGTGTGTGT=1.00 TGTGT=0.00, TGTGTGTGTGT=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 24 TGTGTGTGT=1.00 TGTGT=0.00, TGTGTGTGTGT=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 TGTGTGTGT=1.000 TGTGT=0.000, TGTGTGTGTGT=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 TGTGTGTGT=1.000 TGTGT=0.000, TGTGTGTGTGT=0.000 1.0 0.0 0.0 N/A
South Asian Sub 94 TGTGTGTGT=1.00 TGTGT=0.00, TGTGTGTGTGT=0.00 1.0 0.0 0.0 N/A
Other Sub 470 TGTGTGTGT=1.000 TGTGT=0.000, TGTGTGTGTGT=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
Allele Frequency Aggregator Total Global 11856 (TG)4T=1.00000 delGTGT=0.00000, dupGT=0.00000
Allele Frequency Aggregator European Sub 7618 (TG)4T=1.0000 delGTGT=0.0000, dupGT=0.0000
Allele Frequency Aggregator African Sub 2810 (TG)4T=1.0000 delGTGT=0.0000, dupGT=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 (TG)4T=1.000 delGTGT=0.000, dupGT=0.000
Allele Frequency Aggregator Other Sub 470 (TG)4T=1.000 delGTGT=0.000, dupGT=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 (TG)4T=1.000 delGTGT=0.000, dupGT=0.000
Allele Frequency Aggregator Asian Sub 108 (TG)4T=1.000 delGTGT=0.000, dupGT=0.000
Allele Frequency Aggregator South Asian Sub 94 (TG)4T=1.00 delGTGT=0.00, dupGT=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 17 NC_000017.11:g.40966059GT[2]
GRCh38.p14 chr 17 NC_000017.11:g.40966059GT[5]
GRCh38.p14 chr 17 NC_000017.11:g.40966059GT[6]
GRCh37.p13 chr 17 NC_000017.10:g.39122311GT[2]
GRCh37.p13 chr 17 NC_000017.10:g.39122311GT[5]
GRCh37.p13 chr 17 NC_000017.10:g.39122311GT[6]
KRT39 RefSeqGene NG_012415.1:g.5828CA[2]
KRT39 RefSeqGene NG_012415.1:g.5828CA[5]
KRT39 RefSeqGene NG_012415.1:g.5828CA[6]
GRCh38.p14 chr 17 alt locus HSCHR17_4_CTG4 NW_003871091.1:g.115454GT[2]
GRCh38.p14 chr 17 alt locus HSCHR17_4_CTG4 NW_003871091.1:g.115454GT[5]
GRCh38.p14 chr 17 alt locus HSCHR17_4_CTG4 NW_003871091.1:g.115454GT[6]
Gene: KRT39, keratin 39 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
KRT39 transcript NM_213656.4:c.468+324CA[2] N/A Intron Variant
Gene: LOC107985072, uncharacterized LOC107985072 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC107985072 transcript variant X2 XR_001752885.2:n. N/A Intron Variant
LOC107985072 transcript variant X1 XR_001752886.2:n. 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
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 (TG)4T= delGTGT dupGT dupGTGT
GRCh38.p14 chr 17 NC_000017.11:g.40966058_40966066= NC_000017.11:g.40966059GT[2] NC_000017.11:g.40966059GT[5] NC_000017.11:g.40966059GT[6]
GRCh37.p13 chr 17 NC_000017.10:g.39122310_39122318= NC_000017.10:g.39122311GT[2] NC_000017.10:g.39122311GT[5] NC_000017.10:g.39122311GT[6]
KRT39 RefSeqGene NG_012415.1:g.5827_5835= NG_012415.1:g.5828CA[2] NG_012415.1:g.5828CA[5] NG_012415.1:g.5828CA[6]
GRCh38.p14 chr 17 alt locus HSCHR17_4_CTG4 NW_003871091.1:g.115453_115461= NW_003871091.1:g.115454GT[2] NW_003871091.1:g.115454GT[5] NW_003871091.1:g.115454GT[6]
KRT39 transcript NM_213656.3:c.468+331= NM_213656.3:c.468+324CA[2] NM_213656.3:c.468+324CA[5] NM_213656.3:c.468+324CA[6]
KRT39 transcript NM_213656.4:c.468+331= NM_213656.4:c.468+324CA[2] NM_213656.4:c.468+324CA[5] NM_213656.4:c.468+324CA[6]
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#.

4 SubSNP, 4 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss4311389621 Apr 26, 2021 (155)
2 GNOMAD ss4311389622 Apr 26, 2021 (155)
3 GNOMAD ss4311389623 Apr 26, 2021 (155)
4 HUGCELL_USP ss5496156934 Oct 16, 2022 (156)
5 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 506929654 (NC_000017.11:40966057::TG 4/125418)
Row 506929655 (NC_000017.11:40966057::TGTG 1/125418)
Row 506929656 (NC_000017.11:40966057:TGTG: 69/125414)

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

Submission ignored due to conflicting rows:
Row 506929654 (NC_000017.11:40966057::TG 4/125418)
Row 506929655 (NC_000017.11:40966057::TGTG 1/125418)
Row 506929656 (NC_000017.11:40966057:TGTG: 69/125414)

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

Submission ignored due to conflicting rows:
Row 506929654 (NC_000017.11:40966057::TG 4/125418)
Row 506929655 (NC_000017.11:40966057::TGTG 1/125418)
Row 506929656 (NC_000017.11:40966057:TGTG: 69/125414)

- Apr 26, 2021 (155)
8 ALFA NC_000017.11 - 40966058 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
ss4311389623, ss5496156934 NC_000017.11:40966057:TGTG: NC_000017.11:40966057:TGTGTGTGT:TG…

NC_000017.11:40966057:TGTGTGTGT:TGTGT

(self)
11770034441 NC_000017.11:40966057:TGTGTGTGT:TG…

NC_000017.11:40966057:TGTGTGTGT:TGTGT

NC_000017.11:40966057:TGTGTGTGT:TG…

NC_000017.11:40966057:TGTGTGTGT:TGTGT

(self)
ss4311389621 NC_000017.11:40966057::TG NC_000017.11:40966057:TGTGTGTGT:TG…

NC_000017.11:40966057:TGTGTGTGT:TGTGTGTGTGT

(self)
11770034441 NC_000017.11:40966057:TGTGTGTGT:TG…

NC_000017.11:40966057:TGTGTGTGT:TGTGTGTGTGT

NC_000017.11:40966057:TGTGTGTGT:TG…

NC_000017.11:40966057:TGTGTGTGT:TGTGTGTGTGT

(self)
ss4311389622 NC_000017.11:40966057::TGTG NC_000017.11:40966057:TGTGTGTGT:TG…

NC_000017.11:40966057:TGTGTGTGT:TGTGTGTGTGTGT

(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 rs1204737305

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