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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.

rs1037828930

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr4:127669126 (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
G>A / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.00005 (1/21302, ALFA)
Clinical Significance
Reported in ClinVar
Gene : Consequence
INTU : Stop Gained
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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 21302 G=0.99995 A=0.00005
European Sub 16840 G=1.00000 A=0.00000
African Sub 20 G=1.00 A=0.00
African Others Sub 0 G=0 A=0
African American Sub 20 G=1.00 A=0.00
Asian Sub 0 G=0 A=0
East Asian Sub 0 G=0 A=0
Other Asian Sub 0 G=0 A=0
Latin American 1 Sub 354 G=0.997 A=0.003
Latin American 2 Sub 18 G=1.00 A=0.00
South Asian Sub 0 G=0 A=0
Other Sub 4070 G=1.0000 A=0.0000


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 21302 G=0.99995 A=0.00005
Allele Frequency Aggregator European Sub 16840 G=1.00000 A=0.00000
Allele Frequency Aggregator Other Sub 4070 G=1.0000 A=0.0000
Allele Frequency Aggregator Latin American 1 Sub 354 G=0.997 A=0.003
Allele Frequency Aggregator African Sub 20 G=1.00 A=0.00
Allele Frequency Aggregator Latin American 2 Sub 18 G=1.00 A=0.00
Allele Frequency Aggregator South Asian Sub 0 G=0 A=0
Allele Frequency Aggregator Asian Sub 0 G=0 A=0
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 4 NC_000004.12:g.127669126G>A
GRCh38.p14 chr 4 NC_000004.12:g.127669126G>T
GRCh37.p13 chr 4 NC_000004.11:g.128590281G>A
GRCh37.p13 chr 4 NC_000004.11:g.128590281G>T
Gene: INTU, inturned planar cell polarity protein (plus strand)
Molecule type Change Amino acid[Codon] SO Term
INTU transcript NM_015693.4:c.1063G>A E [GAA] > K [AAA] Coding Sequence Variant
protein inturned NP_056508.2:p.Glu355Lys E (Glu) > K (Lys) Missense Variant
INTU transcript NM_015693.4:c.1063G>T E [GAA] > * [TAA] Coding Sequence Variant
protein inturned NP_056508.2:p.Glu355Ter E (Glu) > * (Ter) Stop Gained
INTU transcript variant X6 XM_011531848.3:c. N/A Genic Upstream Transcript Variant
INTU transcript variant X1 XM_011531844.4:c.1060G>A E [GAA] > K [AAA] Coding Sequence Variant
protein inturned isoform X1 XP_011530146.1:p.Glu354Lys E (Glu) > K (Lys) Missense Variant
INTU transcript variant X1 XM_011531844.4:c.1060G>T E [GAA] > * [TAA] Coding Sequence Variant
protein inturned isoform X1 XP_011530146.1:p.Glu354Ter E (Glu) > * (Ter) Stop Gained
INTU transcript variant X2 XM_011531845.4:c.1063G>A E [GAA] > K [AAA] Coding Sequence Variant
protein inturned isoform X2 XP_011530147.1:p.Glu355Lys E (Glu) > K (Lys) Missense Variant
INTU transcript variant X2 XM_011531845.4:c.1063G>T E [GAA] > * [TAA] Coding Sequence Variant
protein inturned isoform X2 XP_011530147.1:p.Glu355Ter E (Glu) > * (Ter) Stop Gained
INTU transcript variant X3 XM_011531846.2:c.1006G>A E [GAA] > K [AAA] Coding Sequence Variant
protein inturned isoform X3 XP_011530148.1:p.Glu336Lys E (Glu) > K (Lys) Missense Variant
INTU transcript variant X3 XM_011531846.2:c.1006G>T E [GAA] > * [TAA] Coding Sequence Variant
protein inturned isoform X3 XP_011530148.1:p.Glu336Ter E (Glu) > * (Ter) Stop Gained
INTU transcript variant X4 XM_011531847.2:c.67G>A E [GAA] > K [AAA] Coding Sequence Variant
protein inturned isoform X4 XP_011530149.1:p.Glu23Lys E (Glu) > K (Lys) Missense Variant
INTU transcript variant X4 XM_011531847.2:c.67G>T E [GAA] > * [TAA] Coding Sequence Variant
protein inturned isoform X4 XP_011530149.1:p.Glu23Ter E (Glu) > * (Ter) Stop Gained
INTU transcript variant X5 XM_017008025.2:c.67G>A E [GAA] > K [AAA] Coding Sequence Variant
protein inturned isoform X4 XP_016863514.1:p.Glu23Lys E (Glu) > K (Lys) Missense Variant
INTU transcript variant X5 XM_017008025.2:c.67G>T E [GAA] > * [TAA] Coding Sequence Variant
protein inturned isoform X4 XP_016863514.1:p.Glu23Ter E (Glu) > * (Ter) Stop Gained
INTU transcript variant X7 XM_011531849.4:c.1063G>A E [GAA] > K [AAA] Coding Sequence Variant
protein inturned isoform X6 XP_011530151.1:p.Glu355Lys E (Glu) > K (Lys) Missense Variant
INTU transcript variant X7 XM_011531849.4:c.1063G>T E [GAA] > * [TAA] Coding Sequence Variant
protein inturned isoform X6 XP_011530151.1:p.Glu355Ter E (Glu) > * (Ter) Stop Gained
INTU transcript variant X8 XM_011531850.4:c.1063G>A E [GAA] > K [AAA] Coding Sequence Variant
protein inturned isoform X7 XP_011530152.1:p.Glu355Lys E (Glu) > K (Lys) Missense Variant
INTU transcript variant X8 XM_011531850.4:c.1063G>T E [GAA] > * [TAA] Coding Sequence Variant
protein inturned isoform X7 XP_011530152.1:p.Glu355Ter E (Glu) > * (Ter) Stop Gained
INTU transcript variant X9 XM_011531851.4:c.1063G>A E [GAA] > K [AAA] Coding Sequence Variant
protein inturned isoform X8 XP_011530153.1:p.Glu355Lys E (Glu) > K (Lys) Missense Variant
INTU transcript variant X9 XM_011531851.4:c.1063G>T E [GAA] > * [TAA] Coding Sequence Variant
protein inturned isoform X8 XP_011530153.1:p.Glu355Ter E (Glu) > * (Ter) Stop Gained
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.

Allele: T (allele ID: 496106 )
ClinVar Accession Disease Names Clinical Significance
RCV000599556.3 Short-rib thoracic dysplasia 20 with polydactyly Likely-Pathogenic
RCV000851203.1 Short rib-polydactyly syndrome Likely-Pathogenic
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 G= A T
GRCh38.p14 chr 4 NC_000004.12:g.127669126= NC_000004.12:g.127669126G>A NC_000004.12:g.127669126G>T
GRCh37.p13 chr 4 NC_000004.11:g.128590281= NC_000004.11:g.128590281G>A NC_000004.11:g.128590281G>T
INTU transcript NM_015693.4:c.1063= NM_015693.4:c.1063G>A NM_015693.4:c.1063G>T
INTU transcript NM_015693.3:c.1063= NM_015693.3:c.1063G>A NM_015693.3:c.1063G>T
INTU transcript variant X1 XM_011531844.4:c.1060= XM_011531844.4:c.1060G>A XM_011531844.4:c.1060G>T
INTU transcript variant X1 XM_011531844.3:c.1060= XM_011531844.3:c.1060G>A XM_011531844.3:c.1060G>T
INTU transcript variant X1 XM_011531844.2:c.1060= XM_011531844.2:c.1060G>A XM_011531844.2:c.1060G>T
INTU transcript variant X1 XM_011531844.1:c.1060= XM_011531844.1:c.1060G>A XM_011531844.1:c.1060G>T
INTU transcript variant X2 XM_011531845.4:c.1063= XM_011531845.4:c.1063G>A XM_011531845.4:c.1063G>T
INTU transcript variant X2 XM_011531845.3:c.1063= XM_011531845.3:c.1063G>A XM_011531845.3:c.1063G>T
INTU transcript variant X2 XM_011531845.2:c.1063= XM_011531845.2:c.1063G>A XM_011531845.2:c.1063G>T
INTU transcript variant X2 XM_011531845.1:c.1063= XM_011531845.1:c.1063G>A XM_011531845.1:c.1063G>T
INTU transcript variant X9 XM_011531851.4:c.1063= XM_011531851.4:c.1063G>A XM_011531851.4:c.1063G>T
INTU transcript variant X9 XM_011531851.3:c.1063= XM_011531851.3:c.1063G>A XM_011531851.3:c.1063G>T
INTU transcript variant X9 XM_011531851.2:c.1063= XM_011531851.2:c.1063G>A XM_011531851.2:c.1063G>T
INTU transcript variant X8 XM_011531851.1:c.1063= XM_011531851.1:c.1063G>A XM_011531851.1:c.1063G>T
INTU transcript variant X7 XM_011531849.4:c.1063= XM_011531849.4:c.1063G>A XM_011531849.4:c.1063G>T
INTU transcript variant X7 XM_011531849.3:c.1063= XM_011531849.3:c.1063G>A XM_011531849.3:c.1063G>T
INTU transcript variant X7 XM_011531849.2:c.1063= XM_011531849.2:c.1063G>A XM_011531849.2:c.1063G>T
INTU transcript variant X6 XM_011531849.1:c.1063= XM_011531849.1:c.1063G>A XM_011531849.1:c.1063G>T
INTU transcript variant X8 XM_011531850.4:c.1063= XM_011531850.4:c.1063G>A XM_011531850.4:c.1063G>T
INTU transcript variant X8 XM_011531850.3:c.1063= XM_011531850.3:c.1063G>A XM_011531850.3:c.1063G>T
INTU transcript variant X8 XM_011531850.2:c.1063= XM_011531850.2:c.1063G>A XM_011531850.2:c.1063G>T
INTU transcript variant X7 XM_011531850.1:c.1063= XM_011531850.1:c.1063G>A XM_011531850.1:c.1063G>T
INTU transcript variant X3 XM_011531846.2:c.1006= XM_011531846.2:c.1006G>A XM_011531846.2:c.1006G>T
INTU transcript variant X3 XM_011531846.1:c.1006= XM_011531846.1:c.1006G>A XM_011531846.1:c.1006G>T
INTU transcript variant X4 XM_011531847.2:c.67= XM_011531847.2:c.67G>A XM_011531847.2:c.67G>T
INTU transcript variant X4 XM_011531847.1:c.67= XM_011531847.1:c.67G>A XM_011531847.1:c.67G>T
INTU transcript variant X5 XM_017008025.2:c.67= XM_017008025.2:c.67G>A XM_017008025.2:c.67G>T
INTU transcript variant X5 XM_017008025.1:c.67= XM_017008025.1:c.67G>A XM_017008025.1:c.67G>T
protein inturned NP_056508.2:p.Glu355= NP_056508.2:p.Glu355Lys NP_056508.2:p.Glu355Ter
protein inturned isoform X1 XP_011530146.1:p.Glu354= XP_011530146.1:p.Glu354Lys XP_011530146.1:p.Glu354Ter
protein inturned isoform X2 XP_011530147.1:p.Glu355= XP_011530147.1:p.Glu355Lys XP_011530147.1:p.Glu355Ter
protein inturned isoform X8 XP_011530153.1:p.Glu355= XP_011530153.1:p.Glu355Lys XP_011530153.1:p.Glu355Ter
protein inturned isoform X6 XP_011530151.1:p.Glu355= XP_011530151.1:p.Glu355Lys XP_011530151.1:p.Glu355Ter
protein inturned isoform X7 XP_011530152.1:p.Glu355= XP_011530152.1:p.Glu355Lys XP_011530152.1:p.Glu355Ter
protein inturned isoform X3 XP_011530148.1:p.Glu336= XP_011530148.1:p.Glu336Lys XP_011530148.1:p.Glu336Ter
protein inturned isoform X4 XP_011530149.1:p.Glu23= XP_011530149.1:p.Glu23Lys XP_011530149.1:p.Glu23Ter
protein inturned isoform X4 XP_016863514.1:p.Glu23= XP_016863514.1:p.Glu23Lys XP_016863514.1:p.Glu23Ter
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#.

1 SubSNP, 1 Frequency, 2 ClinVar submissions
No Submitter Submission ID Date (Build)
1 HUMAN_LONGEVITY ss2267025484 Dec 20, 2016 (150)
2 ALFA NC_000004.12 - 127669126 Apr 26, 2021 (155)
3 ClinVar RCV000599556.3 Oct 13, 2022 (156)
4 ClinVar RCV000851203.1 Apr 26, 2020 (154)
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
7684352562, ss2267025484 NC_000004.12:127669125:G:A NC_000004.12:127669125:G:A (self)
RCV000599556.3, RCV000851203.1 NC_000004.12:127669125:G:T NC_000004.12:127669125:G:T (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 rs1037828930

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.post761+d5e8e07