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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.

rs1491376274

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr6:37698256-37698257 (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
insC / insCGC / insCGCTCTCC / insC…

insC / insCGC / insCGCTCTCC / insCTCTCGCTCTCC / ins(CT)3CC

Variation Type
Insertion
Frequency
insCTCTCGCTCTCC=0.00031 (5/16028, 8.3KJPN)
insC=0.00000 (0/11850, ALFA)
insCGC=0.00000 (0/11850, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
MDGA1 : 2KB Upstream 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 11850 =1.00000 C=0.00000, CGC=0.00000 1.0 0.0 0.0 N/A
European Sub 7612 =1.0000 C=0.0000, CGC=0.0000 1.0 0.0 0.0 N/A
African Sub 2814 =1.0000 C=0.0000, CGC=0.0000 1.0 0.0 0.0 N/A
African Others Sub 108 =1.000 C=0.000, CGC=0.000 1.0 0.0 0.0 N/A
African American Sub 2706 =1.0000 C=0.0000, CGC=0.0000 1.0 0.0 0.0 N/A
Asian Sub 108 =1.000 C=0.000, CGC=0.000 1.0 0.0 0.0 N/A
East Asian Sub 84 =1.00 C=0.00, CGC=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 24 =1.00 C=0.00, CGC=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 =1.000 C=0.000, CGC=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 606 =1.000 C=0.000, CGC=0.000 1.0 0.0 0.0 N/A
South Asian Sub 94 =1.00 C=0.00, CGC=0.00 1.0 0.0 0.0 N/A
Other Sub 470 =1.000 C=0.000, CGC=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
8.3KJPN JAPANESE Study-wide 16028 -

No frequency provided

insCTCTCGCTCTCC=0.00031
Allele Frequency Aggregator Total Global 11850 -

No frequency provided

insC=0.00000, insCGC=0.00000
Allele Frequency Aggregator European Sub 7612 -

No frequency provided

insC=0.0000, insCGC=0.0000
Allele Frequency Aggregator African Sub 2814 -

No frequency provided

insC=0.0000, insCGC=0.0000
Allele Frequency Aggregator Latin American 2 Sub 606 -

No frequency provided

insC=0.000, insCGC=0.000
Allele Frequency Aggregator Other Sub 470 -

No frequency provided

insC=0.000, insCGC=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 -

No frequency provided

insC=0.000, insCGC=0.000
Allele Frequency Aggregator Asian Sub 108 -

No frequency provided

insC=0.000, insCGC=0.000
Allele Frequency Aggregator South Asian Sub 94 -

No frequency provided

insC=0.00, insCGC=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.37698256_37698257insC
GRCh38.p14 chr 6 NC_000006.12:g.37698256_37698257insCGC
GRCh38.p14 chr 6 NC_000006.12:g.37698256_37698257insCGCTCTCC
GRCh38.p14 chr 6 NC_000006.12:g.37698256_37698257insCTCTCGCTCTCC
GRCh38.p14 chr 6 NC_000006.12:g.37698256_37698257insCTCTCTCC
GRCh37.p13 chr 6 NC_000006.11:g.37666032_37666033insC
GRCh37.p13 chr 6 NC_000006.11:g.37666032_37666033insCGC
GRCh37.p13 chr 6 NC_000006.11:g.37666032_37666033insCGCTCTCC
GRCh37.p13 chr 6 NC_000006.11:g.37666032_37666033insCTCTCGCTCTCC
GRCh37.p13 chr 6 NC_000006.11:g.37666032_37666033insCTCTCTCC
MDGA1 RefSeqGene NG_051764.1:g.4734_4735insG
MDGA1 RefSeqGene NG_051764.1:g.4734_4735insGCG
MDGA1 RefSeqGene NG_051764.1:g.4734_4735insGGAGAGCG
MDGA1 RefSeqGene NG_051764.1:g.4734_4735insGGAGAGCGAGAG
MDGA1 RefSeqGene NG_051764.1:g.4734_4735insGGAGAGAG
Gene: MDGA1, MAM domain containing glycosylphosphatidylinositol anchor 1 (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
MDGA1 transcript NM_153487.4:c. N/A Upstream Transcript Variant
MDGA1 transcript variant X1 XM_006715056.4:c. N/A Upstream Transcript Variant
MDGA1 transcript variant X2 XM_017010734.2:c. N/A Upstream Transcript Variant
MDGA1 transcript variant X3 XM_047418637.1:c. N/A Upstream Transcript Variant
MDGA1 transcript variant X5 XM_047418638.1:c. N/A Upstream Transcript Variant
MDGA1 transcript variant X4 XR_926141.3:n. N/A 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 = insC insCGC insCGCTCTCC insCTCTCGCTCTCC ins(CT)3CC
GRCh38.p14 chr 6 NC_000006.12:g.37698256_37698257= NC_000006.12:g.37698256_37698257insC NC_000006.12:g.37698256_37698257insCGC NC_000006.12:g.37698256_37698257insCGCTCTCC NC_000006.12:g.37698256_37698257insCTCTCGCTCTCC NC_000006.12:g.37698256_37698257insCTCTCTCC
GRCh37.p13 chr 6 NC_000006.11:g.37666032_37666033= NC_000006.11:g.37666032_37666033insC NC_000006.11:g.37666032_37666033insCGC NC_000006.11:g.37666032_37666033insCGCTCTCC NC_000006.11:g.37666032_37666033insCTCTCGCTCTCC NC_000006.11:g.37666032_37666033insCTCTCTCC
MDGA1 RefSeqGene NG_051764.1:g.4734_4735= NG_051764.1:g.4734_4735insG NG_051764.1:g.4734_4735insGCG NG_051764.1:g.4734_4735insGGAGAGCG NG_051764.1:g.4734_4735insGGAGAGCGAGAG NG_051764.1:g.4734_4735insGGAGAGAG
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, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 URBANLAB ss3648330986 Oct 12, 2018 (152)
2 EVA_DECODE ss3717020544 Jul 13, 2019 (153)
3 GNOMAD ss4140090523 Apr 26, 2021 (155)
4 GNOMAD ss4140090524 Apr 26, 2021 (155)
5 GNOMAD ss4140090525 Apr 26, 2021 (155)
6 GNOMAD ss4140090526 Apr 26, 2021 (155)
7 TOMMO_GENOMICS ss5177075915 Apr 26, 2021 (155)
8 TOMMO_GENOMICS ss5714997855 Oct 13, 2022 (156)
9 TOMMO_GENOMICS ss5714997856 Oct 13, 2022 (156)
10 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 222431926 (NC_000006.12:37698256::CGC 6/52546)
Row 222431927 (NC_000006.12:37698256::CGCTCTCC 2/52548)
Row 222431928 (NC_000006.12:37698256::CTCTCGCTCTCC 18/52544)...

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

Submission ignored due to conflicting rows:
Row 222431926 (NC_000006.12:37698256::CGC 6/52546)
Row 222431927 (NC_000006.12:37698256::CGCTCTCC 2/52548)
Row 222431928 (NC_000006.12:37698256::CTCTCGCTCTCC 18/52544)...

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

Submission ignored due to conflicting rows:
Row 222431926 (NC_000006.12:37698256::CGC 6/52546)
Row 222431927 (NC_000006.12:37698256::CGCTCTCC 2/52548)
Row 222431928 (NC_000006.12:37698256::CTCTCGCTCTCC 18/52544)...

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

Submission ignored due to conflicting rows:
Row 222431926 (NC_000006.12:37698256::CGC 6/52546)
Row 222431927 (NC_000006.12:37698256::CGCTCTCC 2/52548)
Row 222431928 (NC_000006.12:37698256::CTCTCGCTCTCC 18/52544)...

- Apr 26, 2021 (155)
14 8.3KJPN NC_000006.11 - 37666033 Apr 26, 2021 (155)
15 14KJPN

Submission ignored due to conflicting rows:
Row 48834959 (NC_000006.12:37698256::CTCTCGCTCTCC 4/23324)
Row 48834960 (NC_000006.12:37698256::CGC 1/23324)

- Oct 13, 2022 (156)
16 14KJPN

Submission ignored due to conflicting rows:
Row 48834959 (NC_000006.12:37698256::CTCTCGCTCTCC 4/23324)
Row 48834960 (NC_000006.12:37698256::CGC 1/23324)

- Oct 13, 2022 (156)
17 ALFA NC_000006.12 - 37698257 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
2070369795, ss3648330986, ss3717020544 NC_000006.12:37698256::C NC_000006.12:37698256::C (self)
2070369795, ss4140090523, ss5714997856 NC_000006.12:37698256::CGC NC_000006.12:37698256::CGC (self)
ss4140090524 NC_000006.12:37698256::CGCTCTCC NC_000006.12:37698256::CGCTCTCC (self)
35045222, ss5177075915 NC_000006.11:37666032::CTCTCGCTCTCC NC_000006.12:37698256::CTCTCGCTCTCC (self)
ss4140090525, ss5714997855 NC_000006.12:37698256::CTCTCGCTCTCC NC_000006.12:37698256::CTCTCGCTCTCC (self)
ss4140090526 NC_000006.12:37698256::CTCTCTCC NC_000006.12:37698256::CTCTCTCC (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 rs1491376274

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