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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.

rs138373747

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:1069009-1069010 (GRCh38.p13) 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
insG / insGC / insGCC / insGCCC
Variation Type
Insertion
Frequency
insG=0.00000 (0/11862, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LOC105378948 : Non Coding Transcript Variant
Publications
0 citations
Genomic View
See rs on genome
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.p13 chr 1 NC_000001.11:g.1069009_1069010insG
GRCh38.p13 chr 1 NC_000001.11:g.1069009_1069010insGC
GRCh38.p13 chr 1 NC_000001.11:g.1069009_1069010insGCC
GRCh38.p13 chr 1 NC_000001.11:g.1069009_1069010insGCCC
GRCh37.p13 chr 1 NC_000001.10:g.1004389_1004390insG
GRCh37.p13 chr 1 NC_000001.10:g.1004389_1004390insGC
GRCh37.p13 chr 1 NC_000001.10:g.1004389_1004390insGCC
GRCh37.p13 chr 1 NC_000001.10:g.1004389_1004390insGCCC
Gene: LOC105378948, uncharacterized LOC105378948 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC105378948 transcript variant 1 NR_168432.1:n.328_329insC N/A Non Coding Transcript Variant
LOC105378948 transcript variant 1 NR_168432.1:n.328_329insGC N/A Non Coding Transcript Variant
LOC105378948 transcript variant 1 NR_168432.1:n.328_329insG…

NR_168432.1:n.328_329insGGC

N/A Non Coding Transcript Variant
LOC105378948 transcript variant 1 NR_168432.1:n.328_329insG…

NR_168432.1:n.328_329insGGGC

N/A Non Coding Transcript Variant
LOC105378948 transcript variant 2 NR_168433.1:n.328_329insC N/A Non Coding Transcript Variant
LOC105378948 transcript variant 2 NR_168433.1:n.328_329insGC N/A Non Coding Transcript Variant
LOC105378948 transcript variant 2 NR_168433.1:n.328_329insG…

NR_168433.1:n.328_329insGGC

N/A Non Coding Transcript Variant
LOC105378948 transcript variant 2 NR_168433.1:n.328_329insG…

NR_168433.1:n.328_329insGGGC

N/A Non Coding 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

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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 11862 =1.00000 G=0.00000
European Sub 7618 =1.0000 G=0.0000
African Sub 2816 =1.0000 G=0.0000
African Others Sub 108 =1.000 G=0.000
African American Sub 2708 =1.0000 G=0.0000
Asian Sub 108 =1.000 G=0.000
East Asian Sub 84 =1.00 G=0.00
Other Asian Sub 24 =1.00 G=0.00
Latin American 1 Sub 146 =1.000 G=0.000
Latin American 2 Sub 610 =1.000 G=0.000
South Asian Sub 94 =1.00 G=0.00
Other Sub 470 =1.000 G=0.000


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 11862 -

No frequency provided

insG=0.00000
Allele Frequency Aggregator European Sub 7618 -

No frequency provided

insG=0.0000
Allele Frequency Aggregator African Sub 2816 -

No frequency provided

insG=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 -

No frequency provided

insG=0.000
Allele Frequency Aggregator Other Sub 470 -

No frequency provided

insG=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 -

No frequency provided

insG=0.000
Allele Frequency Aggregator Asian Sub 108 -

No frequency provided

insG=0.000
Allele Frequency Aggregator South Asian Sub 94 -

No frequency provided

insG=0.00
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 = insG insGC insGCC insGCCC
GRCh38.p13 chr 1 NC_000001.11:g.1069009_1069010= NC_000001.11:g.1069009_1069010insG NC_000001.11:g.1069009_1069010insGC NC_000001.11:g.1069009_1069010insGCC NC_000001.11:g.1069009_1069010insGCCC
GRCh37.p13 chr 1 NC_000001.10:g.1004389_1004390= NC_000001.10:g.1004389_1004390insG NC_000001.10:g.1004389_1004390insGC NC_000001.10:g.1004389_1004390insGCC NC_000001.10:g.1004389_1004390insGCCC
LOC105378948 transcript variant 2 NR_168433.1:n.328_329= NR_168433.1:n.328_329insC NR_168433.1:n.328_329insGC NR_168433.1:n.328_329insGGC NR_168433.1:n.328_329insGGGC
LOC105378948 transcript variant 1 NR_168432.1:n.328_329= NR_168432.1:n.328_329insC NR_168432.1:n.328_329insGC NR_168432.1:n.328_329insGGC NR_168432.1:n.328_329insGGGC
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#.

9 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 TOPMED ss3066460359 Nov 08, 2017 (151)
2 GNOMAD ss3986963250 Apr 25, 2021 (155)
3 GNOMAD ss3986963251 Apr 25, 2021 (155)
4 GNOMAD ss3986963252 Apr 25, 2021 (155)
5 GNOMAD ss3986963253 Apr 25, 2021 (155)
6 TOMMO_GENOMICS ss5142064521 Apr 25, 2021 (155)
7 TOMMO_GENOMICS ss5142064522 Apr 25, 2021 (155)
8 TOMMO_GENOMICS ss5142064523 Apr 25, 2021 (155)
9 TOMMO_GENOMICS ss5142064524 Apr 25, 2021 (155)
10 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 129513 (NC_000001.11:1069009::G 8/117204)
Row 129514 (NC_000001.11:1069009::GC 17/117192)
Row 129515 (NC_000001.11:1069009::GCC 3/117214)...

- Apr 25, 2021 (155)
11 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 129513 (NC_000001.11:1069009::G 8/117204)
Row 129514 (NC_000001.11:1069009::GC 17/117192)
Row 129515 (NC_000001.11:1069009::GCC 3/117214)...

- Apr 25, 2021 (155)
12 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 129513 (NC_000001.11:1069009::G 8/117204)
Row 129514 (NC_000001.11:1069009::GC 17/117192)
Row 129515 (NC_000001.11:1069009::GCC 3/117214)...

- Apr 25, 2021 (155)
13 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 129513 (NC_000001.11:1069009::G 8/117204)
Row 129514 (NC_000001.11:1069009::GC 17/117192)
Row 129515 (NC_000001.11:1069009::GCC 3/117214)...

- Apr 25, 2021 (155)
14 8.3KJPN

Submission ignored due to conflicting rows:
Row 33828 (NC_000001.10:1004389::GC 163/15988)
Row 33829 (NC_000001.10:1004389::GCCC 33/15988)
Row 33830 (NC_000001.10:1004389::G 84/15988)...

- Apr 25, 2021 (155)
15 8.3KJPN

Submission ignored due to conflicting rows:
Row 33828 (NC_000001.10:1004389::GC 163/15988)
Row 33829 (NC_000001.10:1004389::GCCC 33/15988)
Row 33830 (NC_000001.10:1004389::G 84/15988)...

- Apr 25, 2021 (155)
16 8.3KJPN

Submission ignored due to conflicting rows:
Row 33828 (NC_000001.10:1004389::GC 163/15988)
Row 33829 (NC_000001.10:1004389::GCCC 33/15988)
Row 33830 (NC_000001.10:1004389::G 84/15988)...

- Apr 25, 2021 (155)
17 8.3KJPN

Submission ignored due to conflicting rows:
Row 33828 (NC_000001.10:1004389::GC 163/15988)
Row 33829 (NC_000001.10:1004389::GCCC 33/15988)
Row 33830 (NC_000001.10:1004389::G 84/15988)...

- Apr 25, 2021 (155)
18 ALFA NC_000001.11 - 1069010 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).

Associated ID History Updated (Build)
rs369135157 May 15, 2013 (138)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss5142064523 NC_000001.10:1004389::G NC_000001.11:1069009::G
345097356, ss3066460359, ss3986963250 NC_000001.11:1069009::G NC_000001.11:1069009::G (self)
ss5142064521 NC_000001.10:1004389::GC NC_000001.11:1069009::GC
ss3986963251 NC_000001.11:1069009::GC NC_000001.11:1069009::GC
ss5142064524 NC_000001.10:1004389::GCC NC_000001.11:1069009::GCC
ss3986963252 NC_000001.11:1069009::GCC NC_000001.11:1069009::GCC
ss5142064522 NC_000001.10:1004389::GCCC NC_000001.11:1069009::GCCC
ss3986963253 NC_000001.11:1069009::GCCC NC_000001.11:1069009::GCCC
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 rs138373747

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.post596+ae089ad