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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.

rs1490906409

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr13:43879510 (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
C>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.000004 (1/264690, TOPMED)
G=0.000007 (1/140294, GnomAD)
G=0.00000 (0/14050, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CCDC122 : Intron Variant
LACC1 : 5 Prime UTR 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 14050 C=1.00000 G=0.00000 1.0 0.0 0.0 N/A
European Sub 9690 C=1.0000 G=0.0000 1.0 0.0 0.0 N/A
African Sub 2898 C=1.0000 G=0.0000 1.0 0.0 0.0 N/A
African Others Sub 114 C=1.000 G=0.000 1.0 0.0 0.0 N/A
African American Sub 2784 C=1.0000 G=0.0000 1.0 0.0 0.0 N/A
Asian Sub 112 C=1.000 G=0.000 1.0 0.0 0.0 N/A
East Asian Sub 86 C=1.00 G=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 26 C=1.00 G=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 C=1.000 G=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 C=1.000 G=0.000 1.0 0.0 0.0 N/A
South Asian Sub 98 C=1.00 G=0.00 1.0 0.0 0.0 N/A
Other Sub 496 C=1.000 G=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
TopMed Global Study-wide 264690 C=0.999996 G=0.000004
gnomAD - Genomes Global Study-wide 140294 C=0.999993 G=0.000007
gnomAD - Genomes European Sub 75954 C=1.00000 G=0.00000
gnomAD - Genomes African Sub 42068 C=1.00000 G=0.00000
gnomAD - Genomes American Sub 13666 C=1.00000 G=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3320 C=1.0000 G=0.0000
gnomAD - Genomes East Asian Sub 3132 C=0.9997 G=0.0003
gnomAD - Genomes Other Sub 2154 C=1.0000 G=0.0000
Allele Frequency Aggregator Total Global 14050 C=1.00000 G=0.00000
Allele Frequency Aggregator European Sub 9690 C=1.0000 G=0.0000
Allele Frequency Aggregator African Sub 2898 C=1.0000 G=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 C=1.000 G=0.000
Allele Frequency Aggregator Other Sub 496 C=1.000 G=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 C=1.000 G=0.000
Allele Frequency Aggregator Asian Sub 112 C=1.000 G=0.000
Allele Frequency Aggregator South Asian Sub 98 C=1.00 G=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 13 NC_000013.11:g.43879510C>G
GRCh37.p13 chr 13 NC_000013.10:g.44453646C>G
LACC1 RefSeqGene NG_053160.1:g.5677C>G
Gene: CCDC122, coiled-coil domain containing 122 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
CCDC122 transcript variant 1 NM_144974.5:c.-200+121G>C N/A Intron Variant
CCDC122 transcript variant 2 NM_001350617.2:c.-386= N/A 5 Prime UTR Variant
CCDC122 transcript variant 3 NM_001350618.2:c. N/A Genic Upstream Transcript Variant
CCDC122 transcript variant X6 XM_024449324.2:c.-453+121…

XM_024449324.2:c.-453+121G>C

 		N/A Intron Variant
CCDC122 transcript variant X7 XM_024449327.2:c.-404+121…

XM_024449327.2:c.-404+121G>C

 		N/A Intron Variant
CCDC122 transcript variant X3 XM_047430112.1:c.-200+121…

XM_047430112.1:c.-200+121G>C

 		N/A Intron Variant
CCDC122 transcript variant X4 XM_047430113.1:c.-200+121…

XM_047430113.1:c.-200+121G>C

 		N/A Intron Variant
CCDC122 transcript variant X1 XM_017020397.3:c.-292= N/A 5 Prime UTR Variant
CCDC122 transcript variant X2 XM_017020398.2:c.-292= N/A 5 Prime UTR Variant
CCDC122 transcript variant X5 XM_047430114.1:c.-292= N/A 5 Prime UTR Variant
Gene: LACC1, laccase domain containing 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LACC1 transcript variant 1 NM_001128303.2:c.-259= N/A 5 Prime UTR Variant
LACC1 transcript variant 3 NM_001350638.2:c. N/A Genic Upstream Transcript Variant
LACC1 transcript variant 4 NM_001350639.2:c. N/A Genic Upstream Transcript Variant
LACC1 transcript variant 5 NM_001350640.2:c. N/A Genic Upstream Transcript Variant
LACC1 transcript variant 6 NM_001350641.2:c. N/A Genic Upstream Transcript Variant
LACC1 transcript variant 7 NM_001350642.2:c. N/A Genic Upstream Transcript Variant
LACC1 transcript variant 8 NM_001350643.2:c. N/A Genic Upstream Transcript Variant
LACC1 transcript variant 9 NM_001350644.2:c. N/A Genic Upstream Transcript Variant
LACC1 transcript variant 10 NM_001350645.2:c. N/A Genic Upstream Transcript Variant
LACC1 transcript variant 11 NM_001350646.2:c. N/A Genic Upstream Transcript Variant
LACC1 transcript variant 12 NM_001350647.2:c. N/A Genic Upstream Transcript Variant
LACC1 transcript variant 13 NM_001350648.2:c. N/A Genic Upstream Transcript Variant
LACC1 transcript variant 2 NM_153218.4:c. N/A Genic Upstream Transcript Variant
LACC1 transcript variant X4 XM_047430102.1:c.-463= N/A 5 Prime UTR Variant
LACC1 transcript variant X6 XM_047430104.1:c.-259= N/A 5 Prime UTR Variant
LACC1 transcript variant X9 XM_047430106.1:c.-463= N/A 5 Prime UTR Variant
LACC1 transcript variant X11 XM_024449319.2:c.-259= N/A 5 Prime UTR Variant
LACC1 transcript variant X8 XM_011534935.4:c. N/A Genic Upstream Transcript Variant
LACC1 transcript variant X1 XM_047430099.1:c. N/A Genic Upstream Transcript Variant
LACC1 transcript variant X2 XM_047430100.1:c. N/A Genic Upstream Transcript Variant
LACC1 transcript variant X3 XM_047430101.1:c. N/A Genic Upstream Transcript Variant
LACC1 transcript variant X5 XM_047430103.1:c. N/A Genic Upstream Transcript Variant
LACC1 transcript variant X7 XM_047430105.1:c. N/A Genic Upstream Transcript Variant
LACC1 transcript variant X10 XM_047430107.1:c. N/A Genic Upstream Transcript Variant
LACC1 transcript variant X12 XM_047430108.1:c. N/A Genic Upstream Transcript Variant
LACC1 transcript variant X13 XM_047430109.1:c. N/A Genic 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 C= G
GRCh38.p14 chr 13 NC_000013.11:g.43879510= NC_000013.11:g.43879510C>G
GRCh37.p13 chr 13 NC_000013.10:g.44453646= NC_000013.10:g.44453646C>G
LACC1 RefSeqGene NG_053160.1:g.5677= NG_053160.1:g.5677C>G
LACC1 transcript variant 1 NM_001128303.2:c.-259= NM_001128303.2:c.-259C>G
LACC1 transcript variant 1 NM_001128303.1:c.-259= NM_001128303.1:c.-259C>G
CCDC122 transcript variant X1 XM_017020397.3:c.-292= XM_017020397.3:c.-292G>C
CCDC122 transcript variant X1 XM_017020397.2:c.-292= XM_017020397.2:c.-292G>C
CCDC122 transcript variant X1 XM_017020397.1:c.-292= XM_017020397.1:c.-292G>C
LACC1 transcript variant X11 XM_024449319.2:c.-259= XM_024449319.2:c.-259C>G
CCDC122 transcript variant 2 NM_001350617.2:c.-386= NM_001350617.2:c.-386G>C
CCDC122 transcript variant 2 NM_001350617.1:c.-386= NM_001350617.1:c.-386G>C
CCDC122 transcript variant X2 XM_017020398.2:c.-292= XM_017020398.2:c.-292G>C
CCDC122 transcript variant X2 XM_017020398.1:c.-292= XM_017020398.1:c.-292G>C
LACC1 transcript variant 6 NM_001350641.1:c.-472= NM_001350641.1:c.-472C>G
LACC1 transcript variant 3 NM_001350638.1:c.-463= NM_001350638.1:c.-463C>G
LACC1 transcript variant X4 XM_047430102.1:c.-463= XM_047430102.1:c.-463C>G
LACC1 transcript variant 5 NM_001350640.1:c.-268= NM_001350640.1:c.-268C>G
LACC1 transcript variant 10 NM_001350645.1:c.-981= NM_001350645.1:c.-981C>G
LACC1 transcript variant X6 XM_047430104.1:c.-259= XM_047430104.1:c.-259C>G
LACC1 transcript variant 9 NM_001350644.1:c.-777= NM_001350644.1:c.-777C>G
LACC1 transcript variant X9 XM_047430106.1:c.-463= XM_047430106.1:c.-463C>G
CCDC122 transcript variant X5 XM_047430114.1:c.-292= XM_047430114.1:c.-292G>C
CCDC122 transcript NM_144974.3:c.-200+121= NM_144974.3:c.-200+121G>C
CCDC122 transcript variant 1 NM_144974.5:c.-200+121= NM_144974.5:c.-200+121G>C
CCDC122 transcript variant X6 XM_024449324.2:c.-453+121= XM_024449324.2:c.-453+121G>C
CCDC122 transcript variant X7 XM_024449327.2:c.-404+121= XM_024449327.2:c.-404+121G>C
CCDC122 transcript variant X3 XM_047430112.1:c.-200+121= XM_047430112.1:c.-200+121G>C
CCDC122 transcript variant X4 XM_047430113.1:c.-200+121= XM_047430113.1:c.-200+121G>C
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, 3 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss4265087859 Apr 26, 2021 (155)
2 TOPMED ss4944749979 Apr 26, 2021 (155)
3 gnomAD - Genomes NC_000013.11 - 43879510 Apr 26, 2021 (155)
4 TopMed NC_000013.11 - 43879510 Apr 26, 2021 (155)
5 ALFA NC_000013.11 - 43879510 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
429457975, 160295637, 8255341997, ss4265087859, ss4944749979 NC_000013.11:43879509:C:G NC_000013.11:43879509:C:G (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 rs1490906409

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