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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.

rs1490102197

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr6:33178136 (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=0.000004 (1/243804, GnomAD_exome)
T=0.0007 (2/2922, KOREAN)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
COL11A2 : Missense Variant
Publications
0 citations
Genomic View
See rs on genome
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
gnomAD - Exomes Global Study-wide 243804 G=0.999996 A=0.000004
gnomAD - Exomes European Sub 130844 G=1.000000 A=0.000000
gnomAD - Exomes Asian Sub 48048 G=0.99998 A=0.00002
gnomAD - Exomes American Sub 34224 G=1.00000 A=0.00000
gnomAD - Exomes African Sub 15098 G=1.00000 A=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 9608 G=1.0000 A=0.0000
gnomAD - Exomes Other Sub 5982 G=1.0000 A=0.0000
KOREAN population from KRGDB KOREAN Study-wide 2922 G=0.9993 T=0.0007
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.33178136G>A
GRCh38.p14 chr 6 NC_000006.12:g.33178136G>T
GRCh37.p13 chr 6 NC_000006.11:g.33145913G>A
GRCh37.p13 chr 6 NC_000006.11:g.33145913G>T
COL11A2 RefSeqGene NG_011589.1:g.19333C>T
COL11A2 RefSeqGene NG_011589.1:g.19333C>A
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.3:g.4589643G>A
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.3:g.4589643G>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.2:g.4589749G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.2:g.4589749G>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.2:g.4421635G>A
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.2:g.4421635G>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.1:g.4427220G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.1:g.4427220G>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.2:g.4372540G>A
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.2:g.4372540G>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.1:g.4378136G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.1:g.4378136G>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.2:g.4597609G>A
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.2:g.4597609G>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.1:g.4603229G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.1:g.4603229G>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.2:g.4614093G>A
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.2:g.4614093G>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.1:g.4619678G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.1:g.4619678G>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.2:g.4626781G>A
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.2:g.4626781G>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.1:g.4626079G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.1:g.4626079G>T
Gene: COL11A2, collagen type XI alpha 2 chain (minus strand)
Molecule type Change Amino acid[Codon] SO Term
COL11A2 transcript variant 4 NM_001163771.2:c. N/A Genic Downstream Transcript Variant
COL11A2 transcript variant 2 NM_080681.3:c.1610C>T P [CCC] > L [CTC] Coding Sequence Variant
collagen alpha-2(XI) chain isoform 2 preproprotein NP_542412.2:p.Pro537Leu P (Pro) > L (Leu) Missense Variant
COL11A2 transcript variant 2 NM_080681.3:c.1610C>A P [CCC] > H [CAC] Coding Sequence Variant
collagen alpha-2(XI) chain isoform 2 preproprotein NP_542412.2:p.Pro537His P (Pro) > H (His) Missense Variant
COL11A2 transcript variant 1 NM_080680.3:c.1868C>T P [CCC] > L [CTC] Coding Sequence Variant
collagen alpha-2(XI) chain isoform 1 preproprotein NP_542411.2:p.Pro623Leu P (Pro) > L (Leu) Missense Variant
COL11A2 transcript variant 1 NM_080680.3:c.1868C>A P [CCC] > H [CAC] Coding Sequence Variant
collagen alpha-2(XI) chain isoform 1 preproprotein NP_542411.2:p.Pro623His P (Pro) > H (His) Missense Variant
COL11A2 transcript variant 3 NM_080679.3:c.1547C>T P [CCC] > L [CTC] Coding Sequence Variant
collagen alpha-2(XI) chain isoform 3 preproprotein NP_542410.2:p.Pro516Leu P (Pro) > L (Leu) Missense Variant
COL11A2 transcript variant 3 NM_080679.3:c.1547C>A P [CCC] > H [CAC] Coding Sequence Variant
collagen alpha-2(XI) chain isoform 3 preproprotein NP_542410.2:p.Pro516His P (Pro) > H (His) Missense Variant
COL11A2 transcript variant X1 XM_017010250.2:c.1868C>T P [CCC] > L [CTC] Coding Sequence Variant
collagen alpha-2(XI) chain isoform X1 XP_016865739.1:p.Pro623Leu P (Pro) > L (Leu) Missense Variant
COL11A2 transcript variant X1 XM_017010250.2:c.1868C>A P [CCC] > H [CAC] Coding Sequence Variant
collagen alpha-2(XI) chain isoform X1 XP_016865739.1:p.Pro623His P (Pro) > H (His) Missense Variant
COL11A2 transcript variant X2 XM_047418182.1:c.1688C>T P [CCC] > L [CTC] Coding Sequence Variant
collagen alpha-2(XI) chain isoform X2 XP_047274138.1:p.Pro563Leu P (Pro) > L (Leu) Missense Variant
COL11A2 transcript variant X2 XM_047418182.1:c.1688C>A P [CCC] > H [CAC] Coding Sequence Variant
collagen alpha-2(XI) chain isoform X2 XP_047274138.1:p.Pro563His P (Pro) > H (His) Missense Variant
COL11A2 transcript variant X7 XM_047418183.1:c.1022C>T P [CCC] > L [CTC] Coding Sequence Variant
collagen alpha-2(XI) chain isoform X7 XP_047274139.1:p.Pro341Leu P (Pro) > L (Leu) Missense Variant
COL11A2 transcript variant X7 XM_047418183.1:c.1022C>A P [CCC] > H [CAC] Coding Sequence Variant
collagen alpha-2(XI) chain isoform X7 XP_047274139.1:p.Pro341His P (Pro) > H (His) Missense Variant
COL11A2 transcript variant X3 XM_011514299.3:c.1154C>T P [CCC] > L [CTC] Coding Sequence Variant
collagen alpha-2(XI) chain isoform X3 XP_011512601.1:p.Pro385Leu P (Pro) > L (Leu) Missense Variant
COL11A2 transcript variant X3 XM_011514299.3:c.1154C>A P [CCC] > H [CAC] Coding Sequence Variant
collagen alpha-2(XI) chain isoform X3 XP_011512601.1:p.Pro385His P (Pro) > H (His) Missense Variant
COL11A2 transcript variant X4 XM_011514300.3:c.974C>T P [CCC] > L [CTC] Coding Sequence Variant
collagen alpha-2(XI) chain isoform X4 XP_011512602.1:p.Pro325Leu P (Pro) > L (Leu) Missense Variant
COL11A2 transcript variant X4 XM_011514300.3:c.974C>A P [CCC] > H [CAC] Coding Sequence Variant
collagen alpha-2(XI) chain isoform X4 XP_011512602.1:p.Pro325His P (Pro) > H (His) Missense Variant
COL11A2 transcript variant X5 XM_011514302.3:c.755C>T P [CCC] > L [CTC] Coding Sequence Variant
collagen alpha-2(XI) chain isoform X5 XP_011512604.1:p.Pro252Leu P (Pro) > L (Leu) Missense Variant
COL11A2 transcript variant X5 XM_011514302.3:c.755C>A P [CCC] > H [CAC] Coding Sequence Variant
collagen alpha-2(XI) chain isoform X5 XP_011512604.1:p.Pro252His P (Pro) > H (His) Missense Variant
COL11A2 transcript variant X6 XM_017010251.3:c.686C>T P [CCC] > L [CTC] Coding Sequence Variant
collagen alpha-2(XI) chain isoform X6 XP_016865740.1:p.Pro229Leu P (Pro) > L (Leu) Missense Variant
COL11A2 transcript variant X6 XM_017010251.3:c.686C>A P [CCC] > H [CAC] Coding Sequence Variant
collagen alpha-2(XI) chain isoform X6 XP_016865740.1:p.Pro229His P (Pro) > H (His) Missense 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 G= A T
GRCh38.p14 chr 6 NC_000006.12:g.33178136= NC_000006.12:g.33178136G>A NC_000006.12:g.33178136G>T
GRCh37.p13 chr 6 NC_000006.11:g.33145913= NC_000006.11:g.33145913G>A NC_000006.11:g.33145913G>T
COL11A2 RefSeqGene NG_011589.1:g.19333= NG_011589.1:g.19333C>T NG_011589.1:g.19333C>A
COL11A2 transcript variant 1 NM_080680.3:c.1868= NM_080680.3:c.1868C>T NM_080680.3:c.1868C>A
COL11A2 transcript variant 1 NM_080680.2:c.1868= NM_080680.2:c.1868C>T NM_080680.2:c.1868C>A
COL11A2 transcript variant 2 NM_080681.3:c.1610= NM_080681.3:c.1610C>T NM_080681.3:c.1610C>A
COL11A2 transcript variant 2 NM_080681.2:c.1610= NM_080681.2:c.1610C>T NM_080681.2:c.1610C>A
COL11A2 transcript variant 3 NM_080679.3:c.1547= NM_080679.3:c.1547C>T NM_080679.3:c.1547C>A
COL11A2 transcript variant 3 NM_080679.2:c.1547= NM_080679.2:c.1547C>T NM_080679.2:c.1547C>A
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.3:g.4589643= NT_113891.3:g.4589643G>A NT_113891.3:g.4589643G>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.2:g.4589749= NT_113891.2:g.4589749G>A NT_113891.2:g.4589749G>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.2:g.4421635= NT_167245.2:g.4421635G>A NT_167245.2:g.4421635G>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.1:g.4427220= NT_167245.1:g.4427220G>A NT_167245.1:g.4427220G>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.2:g.4372540= NT_167248.2:g.4372540G>A NT_167248.2:g.4372540G>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.1:g.4378136= NT_167248.1:g.4378136G>A NT_167248.1:g.4378136G>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.2:g.4597609= NT_167246.2:g.4597609G>A NT_167246.2:g.4597609G>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.1:g.4603229= NT_167246.1:g.4603229G>A NT_167246.1:g.4603229G>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.2:g.4614093= NT_167247.2:g.4614093G>A NT_167247.2:g.4614093G>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.1:g.4619678= NT_167247.1:g.4619678G>A NT_167247.1:g.4619678G>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.2:g.4626781= NT_167249.2:g.4626781G>A NT_167249.2:g.4626781G>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.1:g.4626079= NT_167249.1:g.4626079G>A NT_167249.1:g.4626079G>T
COL11A2 transcript variant X3 XM_011514299.3:c.1154= XM_011514299.3:c.1154C>T XM_011514299.3:c.1154C>A
COL11A2 transcript variant X2 XM_011514299.2:c.1154= XM_011514299.2:c.1154C>T XM_011514299.2:c.1154C>A
COL11A2 transcript variant X2 XM_011514299.1:c.1154= XM_011514299.1:c.1154C>T XM_011514299.1:c.1154C>A
COL11A2 transcript variant X5 XM_011514302.3:c.755= XM_011514302.3:c.755C>T XM_011514302.3:c.755C>A
COL11A2 transcript variant X4 XM_011514302.2:c.755= XM_011514302.2:c.755C>T XM_011514302.2:c.755C>A
COL11A2 transcript variant X5 XM_011514302.1:c.755= XM_011514302.1:c.755C>T XM_011514302.1:c.755C>A
COL11A2 transcript variant X4 XM_011514300.3:c.974= XM_011514300.3:c.974C>T XM_011514300.3:c.974C>A
COL11A2 transcript variant X3 XM_011514300.2:c.974= XM_011514300.2:c.974C>T XM_011514300.2:c.974C>A
COL11A2 transcript variant X3 XM_011514300.1:c.974= XM_011514300.1:c.974C>T XM_011514300.1:c.974C>A
COL11A2 transcript variant X6 XM_017010251.3:c.686= XM_017010251.3:c.686C>T XM_017010251.3:c.686C>A
COL11A2 transcript variant X5 XM_017010251.2:c.686= XM_017010251.2:c.686C>T XM_017010251.2:c.686C>A
COL11A2 transcript variant X5 XM_017010251.1:c.686= XM_017010251.1:c.686C>T XM_017010251.1:c.686C>A
COL11A2 transcript variant X1 XM_017010250.2:c.1868= XM_017010250.2:c.1868C>T XM_017010250.2:c.1868C>A
COL11A2 transcript variant X1 XM_017010250.1:c.1868= XM_017010250.1:c.1868C>T XM_017010250.1:c.1868C>A
COL11A2 transcript variant X7 XM_047418183.1:c.1022= XM_047418183.1:c.1022C>T XM_047418183.1:c.1022C>A
COL11A2 transcript variant X2 XM_047418182.1:c.1688= XM_047418182.1:c.1688C>T XM_047418182.1:c.1688C>A
collagen alpha-2(XI) chain isoform 1 preproprotein NP_542411.2:p.Pro623= NP_542411.2:p.Pro623Leu NP_542411.2:p.Pro623His
collagen alpha-2(XI) chain isoform 2 preproprotein NP_542412.2:p.Pro537= NP_542412.2:p.Pro537Leu NP_542412.2:p.Pro537His
collagen alpha-2(XI) chain isoform 3 preproprotein NP_542410.2:p.Pro516= NP_542410.2:p.Pro516Leu NP_542410.2:p.Pro516His
collagen alpha-2(XI) chain isoform X3 XP_011512601.1:p.Pro385= XP_011512601.1:p.Pro385Leu XP_011512601.1:p.Pro385His
collagen alpha-2(XI) chain isoform X5 XP_011512604.1:p.Pro252= XP_011512604.1:p.Pro252Leu XP_011512604.1:p.Pro252His
collagen alpha-2(XI) chain isoform X4 XP_011512602.1:p.Pro325= XP_011512602.1:p.Pro325Leu XP_011512602.1:p.Pro325His
collagen alpha-2(XI) chain isoform X6 XP_016865740.1:p.Pro229= XP_016865740.1:p.Pro229Leu XP_016865740.1:p.Pro229His
collagen alpha-2(XI) chain isoform X1 XP_016865739.1:p.Pro623= XP_016865739.1:p.Pro623Leu XP_016865739.1:p.Pro623His
collagen alpha-2(XI) chain isoform X7 XP_047274139.1:p.Pro341= XP_047274139.1:p.Pro341Leu XP_047274139.1:p.Pro341His
collagen alpha-2(XI) chain isoform X2 XP_047274138.1:p.Pro563= XP_047274138.1:p.Pro563Leu XP_047274138.1:p.Pro563His
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#.

2 SubSNP, 2 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss2735702378 Nov 08, 2017 (151)
2 KRGDB ss3911092868 Apr 26, 2020 (154)
3 gnomAD - Exomes NC_000006.11 - 33145913 Jul 13, 2019 (153)
4 KOREAN population from KRGDB NC_000006.11 - 33145913 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
4843978, ss2735702378 NC_000006.11:33145912:G:A NC_000006.12:33178135:G:A (self)
18270262, ss3911092868 NC_000006.11:33145912:G:T NC_000006.12:33178135: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 rs1490102197

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