Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

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.

rs1483758478

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr8:138725428 (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>C
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000008 (2/264690, TOPMED)
A=0.000014 (2/140260, GnomAD)
A=0.00000 (0/10680, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
COL22A1 : Missense 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 26952 G=0.99996 A=0.00004 0.999926 0.0 7.4e-05 0
European Sub 16992 G=1.00000 A=0.00000 1.0 0.0 0.0 N/A
African Sub 7118 G=0.9999 A=0.0001 0.999719 0.0 0.000281 0
African Others Sub 268 G=1.000 A=0.000 1.0 0.0 0.0 N/A
African American Sub 6850 G=0.9999 A=0.0001 0.999708 0.0 0.000292 0
Asian Sub 108 G=1.000 A=0.000 1.0 0.0 0.0 N/A
East Asian Sub 84 G=1.00 A=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 24 G=1.00 A=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 G=1.000 A=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 G=1.000 A=0.000 1.0 0.0 0.0 N/A
South Asian Sub 94 G=1.00 A=0.00 1.0 0.0 0.0 N/A
Other Sub 1884 G=1.0000 A=0.0000 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
TopMed Global Study-wide 264690 G=0.999992 A=0.000008
gnomAD - Genomes Global Study-wide 140260 G=0.999986 A=0.000014
gnomAD - Genomes European Sub 75964 G=1.00000 A=0.00000
gnomAD - Genomes African Sub 42022 G=0.99995 A=0.00005
gnomAD - Genomes American Sub 13666 G=1.00000 A=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3322 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3132 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2154 G=1.0000 A=0.0000
Allele Frequency Aggregator Total Global 10680 G=1.00000 A=0.00000
Allele Frequency Aggregator European Sub 6962 G=1.0000 A=0.0000
Allele Frequency Aggregator African Sub 2294 G=1.0000 A=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 G=1.000 A=0.000
Allele Frequency Aggregator Other Sub 466 G=1.000 A=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 G=1.000 A=0.000
Allele Frequency Aggregator Asian Sub 108 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 94 G=1.00 A=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 8 NC_000008.11:g.138725428G>A
GRCh38.p14 chr 8 NC_000008.11:g.138725428G>C
GRCh37.p13 chr 8 NC_000008.10:g.139737671G>A
GRCh37.p13 chr 8 NC_000008.10:g.139737671G>C
COL22A1 RefSeqGene NG_054761.1:g.193660C>T
COL22A1 RefSeqGene NG_054761.1:g.193660C>G
Gene: COL22A1, collagen type XXII alpha 1 chain (minus strand)
Molecule type Change Amino acid[Codon] SO Term
COL22A1 transcript NM_152888.3:c.2152C>T P [CCC] > S [TCC] Coding Sequence Variant
collagen alpha-1(XXII) chain precursor NP_690848.1:p.Pro718Ser P (Pro) > S (Ser) Missense Variant
COL22A1 transcript NM_152888.3:c.2152C>G P [CCC] > A [GCC] Coding Sequence Variant
collagen alpha-1(XXII) chain precursor NP_690848.1:p.Pro718Ala P (Pro) > A (Ala) Missense Variant
COL22A1 transcript variant X6 XM_017013151.2:c.2140-463…

XM_017013151.2:c.2140-4636C>T

 		N/A Intron Variant
COL22A1 transcript variant X7 XM_011516887.2:c.1126C>T P [CCC] > S [TCC] Coding Sequence Variant
collagen alpha-1(XXII) chain isoform X7 XP_011515189.1:p.Pro376Ser P (Pro) > S (Ser) Missense Variant
COL22A1 transcript variant X7 XM_011516887.2:c.1126C>G P [CCC] > A [GCC] Coding Sequence Variant
collagen alpha-1(XXII) chain isoform X7 XP_011515189.1:p.Pro376Ala P (Pro) > A (Ala) Missense Variant
COL22A1 transcript variant X1 XM_011516883.3:c.2152C>T P [CCC] > S [TCC] Coding Sequence Variant
collagen alpha-1(XXII) chain isoform X1 XP_011515185.1:p.Pro718Ser P (Pro) > S (Ser) Missense Variant
COL22A1 transcript variant X1 XM_011516883.3:c.2152C>G P [CCC] > A [GCC] Coding Sequence Variant
collagen alpha-1(XXII) chain isoform X1 XP_011515185.1:p.Pro718Ala P (Pro) > A (Ala) Missense Variant
COL22A1 transcript variant X2 XM_011516884.3:c.2113C>T P [CCC] > S [TCC] Coding Sequence Variant
collagen alpha-1(XXII) chain isoform X2 XP_011515186.1:p.Pro705Ser P (Pro) > S (Ser) Missense Variant
COL22A1 transcript variant X2 XM_011516884.3:c.2113C>G P [CCC] > A [GCC] Coding Sequence Variant
collagen alpha-1(XXII) chain isoform X2 XP_011515186.1:p.Pro705Ala P (Pro) > A (Ala) Missense Variant
COL22A1 transcript variant X3 XM_011516885.3:c.2152C>T P [CCC] > S [TCC] Coding Sequence Variant
collagen alpha-1(XXII) chain isoform X3 XP_011515187.1:p.Pro718Ser P (Pro) > S (Ser) Missense Variant
COL22A1 transcript variant X3 XM_011516885.3:c.2152C>G P [CCC] > A [GCC] Coding Sequence Variant
collagen alpha-1(XXII) chain isoform X3 XP_011515187.1:p.Pro718Ala P (Pro) > A (Ala) Missense Variant
COL22A1 transcript variant X4 XM_011516886.4:c.2065C>T P [CCC] > S [TCC] Coding Sequence Variant
collagen alpha-1(XXII) chain isoform X4 XP_011515188.1:p.Pro689Ser P (Pro) > S (Ser) Missense Variant
COL22A1 transcript variant X4 XM_011516886.4:c.2065C>G P [CCC] > A [GCC] Coding Sequence Variant
collagen alpha-1(XXII) chain isoform X4 XP_011515188.1:p.Pro689Ala P (Pro) > A (Ala) Missense Variant
COL22A1 transcript variant X5 XM_017013150.3:c.2026C>T P [CCC] > S [TCC] Coding Sequence Variant
collagen alpha-1(XXII) chain isoform X5 XP_016868639.1:p.Pro676Ser P (Pro) > S (Ser) Missense Variant
COL22A1 transcript variant X5 XM_017013150.3:c.2026C>G P [CCC] > A [GCC] Coding Sequence Variant
collagen alpha-1(XXII) chain isoform X5 XP_016868639.1:p.Pro676Ala P (Pro) > A (Ala) Missense Variant
COL22A1 transcript variant X8 XM_017013152.2:c.1126C>T P [CCC] > S [TCC] Coding Sequence Variant
collagen alpha-1(XXII) chain isoform X7 XP_016868641.1:p.Pro376Ser P (Pro) > S (Ser) Missense Variant
COL22A1 transcript variant X8 XM_017013152.2:c.1126C>G P [CCC] > A [GCC] Coding Sequence Variant
collagen alpha-1(XXII) chain isoform X7 XP_016868641.1:p.Pro376Ala P (Pro) > A (Ala) Missense Variant
COL22A1 transcript variant X9 XM_011516888.3:c.2152C>T P [CCC] > S [TCC] Coding Sequence Variant
collagen alpha-1(XXII) chain isoform X8 XP_011515190.1:p.Pro718Ser P (Pro) > S (Ser) Missense Variant
COL22A1 transcript variant X9 XM_011516888.3:c.2152C>G P [CCC] > A [GCC] Coding Sequence Variant
collagen alpha-1(XXII) chain isoform X8 XP_011515190.1:p.Pro718Ala P (Pro) > A (Ala) Missense Variant
COL22A1 transcript variant X10 XM_047421412.1:c.2152C>T P [CCC] > S [TCC] Coding Sequence Variant
collagen alpha-1(XXII) chain isoform X9 XP_047277368.1:p.Pro718Ser P (Pro) > S (Ser) Missense Variant
COL22A1 transcript variant X10 XM_047421412.1:c.2152C>G P [CCC] > A [GCC] Coding Sequence Variant
collagen alpha-1(XXII) chain isoform X9 XP_047277368.1:p.Pro718Ala P (Pro) > A (Ala) Missense Variant
COL22A1 transcript variant X11 XM_011516889.3:c.508C>T P [CCC] > S [TCC] Coding Sequence Variant
collagen alpha-1(XXII) chain isoform X10 XP_011515191.1:p.Pro170Ser P (Pro) > S (Ser) Missense Variant
COL22A1 transcript variant X11 XM_011516889.3:c.508C>G P [CCC] > A [GCC] Coding Sequence Variant
collagen alpha-1(XXII) chain isoform X10 XP_011515191.1:p.Pro170Ala P (Pro) > A (Ala) Missense Variant
COL22A1 transcript variant X12 XR_001745487.2:n.2637C>T N/A Non Coding Transcript Variant
COL22A1 transcript variant X12 XR_001745487.2:n.2637C>G 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
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 C
GRCh38.p14 chr 8 NC_000008.11:g.138725428= NC_000008.11:g.138725428G>A NC_000008.11:g.138725428G>C
GRCh37.p13 chr 8 NC_000008.10:g.139737671= NC_000008.10:g.139737671G>A NC_000008.10:g.139737671G>C
COL22A1 RefSeqGene NG_054761.1:g.193660= NG_054761.1:g.193660C>T NG_054761.1:g.193660C>G
COL22A1 transcript NM_152888.3:c.2152= NM_152888.3:c.2152C>T NM_152888.3:c.2152C>G
COL22A1 transcript NM_152888.2:c.2152= NM_152888.2:c.2152C>T NM_152888.2:c.2152C>G
COL22A1 transcript NM_152888.1:c.2152= NM_152888.1:c.2152C>T NM_152888.1:c.2152C>G
COL22A1 transcript variant X4 XM_011516886.4:c.2065= XM_011516886.4:c.2065C>T XM_011516886.4:c.2065C>G
COL22A1 transcript variant X4 XM_011516886.3:c.2065= XM_011516886.3:c.2065C>T XM_011516886.3:c.2065C>G
COL22A1 transcript variant X4 XM_011516886.2:c.2065= XM_011516886.2:c.2065C>T XM_011516886.2:c.2065C>G
COL22A1 transcript variant X4 XM_011516886.1:c.2065= XM_011516886.1:c.2065C>T XM_011516886.1:c.2065C>G
COL22A1 transcript variant X1 XM_011516883.3:c.2152= XM_011516883.3:c.2152C>T XM_011516883.3:c.2152C>G
COL22A1 transcript variant X1 XM_011516883.2:c.2152= XM_011516883.2:c.2152C>T XM_011516883.2:c.2152C>G
COL22A1 transcript variant X1 XM_011516883.1:c.2152= XM_011516883.1:c.2152C>T XM_011516883.1:c.2152C>G
COL22A1 transcript variant X2 XM_011516884.3:c.2113= XM_011516884.3:c.2113C>T XM_011516884.3:c.2113C>G
COL22A1 transcript variant X2 XM_011516884.2:c.2113= XM_011516884.2:c.2113C>T XM_011516884.2:c.2113C>G
COL22A1 transcript variant X2 XM_011516884.1:c.2113= XM_011516884.1:c.2113C>T XM_011516884.1:c.2113C>G
COL22A1 transcript variant X3 XM_011516885.3:c.2152= XM_011516885.3:c.2152C>T XM_011516885.3:c.2152C>G
COL22A1 transcript variant X3 XM_011516885.2:c.2152= XM_011516885.2:c.2152C>T XM_011516885.2:c.2152C>G
COL22A1 transcript variant X3 XM_011516885.1:c.2152= XM_011516885.1:c.2152C>T XM_011516885.1:c.2152C>G
COL22A1 transcript variant X5 XM_017013150.3:c.2026= XM_017013150.3:c.2026C>T XM_017013150.3:c.2026C>G
COL22A1 transcript variant X5 XM_017013150.2:c.2026= XM_017013150.2:c.2026C>T XM_017013150.2:c.2026C>G
COL22A1 transcript variant X5 XM_017013150.1:c.2026= XM_017013150.1:c.2026C>T XM_017013150.1:c.2026C>G
COL22A1 transcript variant X9 XM_011516888.3:c.2152= XM_011516888.3:c.2152C>T XM_011516888.3:c.2152C>G
COL22A1 transcript variant X9 XM_011516888.2:c.2152= XM_011516888.2:c.2152C>T XM_011516888.2:c.2152C>G
COL22A1 transcript variant X6 XM_011516888.1:c.2152= XM_011516888.1:c.2152C>T XM_011516888.1:c.2152C>G
COL22A1 transcript variant X11 XM_011516889.3:c.508= XM_011516889.3:c.508C>T XM_011516889.3:c.508C>G
COL22A1 transcript variant X10 XM_011516889.2:c.508= XM_011516889.2:c.508C>T XM_011516889.2:c.508C>G
COL22A1 transcript variant X7 XM_011516889.1:c.508= XM_011516889.1:c.508C>T XM_011516889.1:c.508C>G
COL22A1 transcript variant X7 XM_011516887.2:c.1126= XM_011516887.2:c.1126C>T XM_011516887.2:c.1126C>G
COL22A1 transcript variant X5 XM_011516887.1:c.1126= XM_011516887.1:c.1126C>T XM_011516887.1:c.1126C>G
COL22A1 transcript variant X8 XM_017013152.2:c.1126= XM_017013152.2:c.1126C>T XM_017013152.2:c.1126C>G
COL22A1 transcript variant X8 XM_017013152.1:c.1126= XM_017013152.1:c.1126C>T XM_017013152.1:c.1126C>G
COL22A1 transcript variant X12 XR_001745487.2:n.2637= XR_001745487.2:n.2637C>T XR_001745487.2:n.2637C>G
COL22A1 transcript variant X11 XR_001745487.1:n.2683= XR_001745487.1:n.2683C>T XR_001745487.1:n.2683C>G
COL22A1 transcript variant X10 XM_047421412.1:c.2152= XM_047421412.1:c.2152C>T XM_047421412.1:c.2152C>G
collagen alpha-1(XXII) chain precursor NP_690848.1:p.Pro718= NP_690848.1:p.Pro718Ser NP_690848.1:p.Pro718Ala
collagen alpha-1(XXII) chain isoform X4 XP_011515188.1:p.Pro689= XP_011515188.1:p.Pro689Ser XP_011515188.1:p.Pro689Ala
collagen alpha-1(XXII) chain isoform X1 XP_011515185.1:p.Pro718= XP_011515185.1:p.Pro718Ser XP_011515185.1:p.Pro718Ala
collagen alpha-1(XXII) chain isoform X2 XP_011515186.1:p.Pro705= XP_011515186.1:p.Pro705Ser XP_011515186.1:p.Pro705Ala
collagen alpha-1(XXII) chain isoform X3 XP_011515187.1:p.Pro718= XP_011515187.1:p.Pro718Ser XP_011515187.1:p.Pro718Ala
collagen alpha-1(XXII) chain isoform X5 XP_016868639.1:p.Pro676= XP_016868639.1:p.Pro676Ser XP_016868639.1:p.Pro676Ala
collagen alpha-1(XXII) chain isoform X8 XP_011515190.1:p.Pro718= XP_011515190.1:p.Pro718Ser XP_011515190.1:p.Pro718Ala
collagen alpha-1(XXII) chain isoform X10 XP_011515191.1:p.Pro170= XP_011515191.1:p.Pro170Ser XP_011515191.1:p.Pro170Ala
collagen alpha-1(XXII) chain isoform X7 XP_011515189.1:p.Pro376= XP_011515189.1:p.Pro376Ser XP_011515189.1:p.Pro376Ala
collagen alpha-1(XXII) chain isoform X7 XP_016868641.1:p.Pro376= XP_016868641.1:p.Pro376Ser XP_016868641.1:p.Pro376Ala
collagen alpha-1(XXII) chain isoform X9 XP_047277368.1:p.Pro718= XP_047277368.1:p.Pro718Ser XP_047277368.1:p.Pro718Ala
COL22A1 transcript variant X6 XM_017013151.2:c.2140-4636= XM_017013151.2:c.2140-4636C>T XM_017013151.2:c.2140-4636C>G
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, 5 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss2737367538 Nov 08, 2017 (151)
2 KOEX ss3029673628 Nov 08, 2017 (151)
3 GNOMAD ss4194877937 Apr 26, 2021 (155)
4 TOPMED ss4807109372 Apr 26, 2021 (155)
5 gnomAD - Genomes NC_000008.11 - 138725428 Apr 26, 2021 (155)
6 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 6543662 (NC_000008.10:139737670:G:G 250927/250928, NC_000008.10:139737670:G:A 1/250928)
Row 6543663 (NC_000008.10:139737670:G:G 250927/250928, NC_000008.10:139737670:G:C 1/250928)

- Jul 13, 2019 (153)
7 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 6543662 (NC_000008.10:139737670:G:G 250927/250928, NC_000008.10:139737670:G:A 1/250928)
Row 6543663 (NC_000008.10:139737670:G:G 250927/250928, NC_000008.10:139737670:G:C 1/250928)

- Jul 13, 2019 (153)
8 TopMed NC_000008.11 - 138725428 Apr 26, 2021 (155)
9 ALFA NC_000008.11 - 138725428 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
ss2737367538, ss3029673628 NC_000008.10:139737670:G:A NC_000008.11:138725427:G:A (self)
313572547, 644486932, 8016569169, ss4194877937, ss4807109372 NC_000008.11:138725427:G:A NC_000008.11:138725427:G:A (self)
NC_000008.10:139737670:G:C NC_000008.11:138725427:G:C (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 rs1483758478

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