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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.

rs1489639613

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:147204986 (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 (1/140268, GnomAD)
G=0.00000 (0/14050, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
FMO5 : Missense Variant
CHD1L : Intron 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 140268 C=0.999993 G=0.000007
gnomAD - Genomes European Sub 75946 C=0.99999 G=0.00001
gnomAD - Genomes African Sub 42048 C=1.00000 G=0.00000
gnomAD - Genomes American Sub 13666 C=1.00000 G=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3324 C=1.0000 G=0.0000
gnomAD - Genomes East Asian Sub 3132 C=1.0000 G=0.0000
gnomAD - Genomes Other Sub 2152 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 1 NC_000001.11:g.147204986C>G
GRCh37.p13 chr 1 fix patch HG1287_PATCH NW_003871055.3:g.4020399C>G
CCT8P1 pseudogene NG_016732.3:g.99G>C
CHD1L RefSeqGene NG_052905.1:g.36793C>G
GRCh37.p13 chr 1 NC_000001.10:g.146676567C>G
Gene: FMO5, flavin containing dimethylaniline monoxygenase 5 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
FMO5 transcript variant 2 NM_001144829.3:c.831-3482…

NM_001144829.3:c.831-3482G>C

 		N/A Intron Variant
FMO5 transcript variant 3 NM_001144830.3:c.830+3866…

NM_001144830.3:c.830+3866G>C

 		N/A Intron Variant
FMO5 transcript variant 1 NM_001461.4:c.831-3482G>C N/A Intron Variant
FMO5 transcript variant X1 XM_005272946.6:c.831-3482…

XM_005272946.6:c.831-3482G>C

 		N/A Intron Variant
FMO5 transcript variant X4 XM_005272947.6:c.831-3482…

XM_005272947.6:c.831-3482G>C

 		N/A Intron Variant
FMO5 transcript variant X3 XM_005272948.6:c.831-3482…

XM_005272948.6:c.831-3482G>C

 		N/A Intron Variant
FMO5 transcript variant X2 XM_011509350.4:c.831-3482…

XM_011509350.4:c.831-3482G>C

 		N/A Intron Variant
FMO5 transcript variant X5 XM_011509351.4:c.642-3482…

XM_011509351.4:c.642-3482G>C

 		N/A Intron Variant
FMO5 transcript variant X7 XM_017000801.3:c.642-3482…

XM_017000801.3:c.642-3482G>C

 		N/A Intron Variant
FMO5 transcript variant X8 XM_017000802.3:c.642-3482…

XM_017000802.3:c.642-3482G>C

 		N/A Intron Variant
FMO5 transcript variant X6 XM_047416250.1:c.642-3482…

XM_047416250.1:c.642-3482G>C

 		N/A Intron Variant
FMO5 transcript variant X9 XM_006711244.5:c.854G>C W [TGG] > S [TCG] Coding Sequence Variant
flavin-containing monooxygenase 5 isoform X3 XP_006711307.1:p.Trp285Ser W (Trp) > S (Ser) Missense Variant
FMO5 transcript variant X10 XM_047416274.1:c.854G>C W [TGG] > S [TCG] Coding Sequence Variant
flavin-containing monooxygenase 5 isoform X3 XP_047272230.1:p.Trp285Ser W (Trp) > S (Ser) Missense Variant
FMO5 transcript variant X11 XM_047416278.1:c.854G>C W [TGG] > S [TCG] Coding Sequence Variant
flavin-containing monooxygenase 5 isoform X3 XP_047272234.1:p.Trp285Ser W (Trp) > S (Ser) Missense Variant
FMO5 transcript variant X12 XM_047416285.1:c.854G>C W [TGG] > S [TCG] Coding Sequence Variant
flavin-containing monooxygenase 5 isoform X3 XP_047272241.1:p.Trp285Ser W (Trp) > S (Ser) Missense Variant
FMO5 transcript variant X13 XM_047416292.1:c.665G>C W [TGG] > S [TCG] Coding Sequence Variant
flavin-containing monooxygenase 5 isoform X4 XP_047272248.1:p.Trp222Ser W (Trp) > S (Ser) Missense Variant
Gene: CHD1L, chromodomain helicase DNA binding protein 1 like (plus strand)
Molecule type Change Amino acid[Codon] SO Term
CHD1L transcript variant 7 NM_001348451.2:c.-90+3040…

NM_001348451.2:c.-90+30401C>G

 		N/A Intron Variant
CHD1L transcript variant 2 NM_001256336.3:c. N/A Genic Upstream Transcript Variant
CHD1L transcript variant 4 NM_001256337.3:c. N/A Genic Upstream Transcript Variant
CHD1L transcript variant 5 NM_001256338.3:c. N/A Genic Upstream Transcript Variant
CHD1L transcript variant 8 NM_001348452.2:c. N/A Genic Upstream Transcript Variant
CHD1L transcript variant 9 NM_001348453.2:c. N/A Genic Upstream Transcript Variant
CHD1L transcript variant 10 NM_001348454.2:c. N/A Genic Upstream Transcript Variant
CHD1L transcript variant 11 NM_001348455.2:c. N/A Genic Upstream Transcript Variant
CHD1L transcript variant 12 NM_001348456.2:c. N/A Genic Upstream Transcript Variant
CHD1L transcript variant 13 NM_001348457.2:c. N/A Genic Upstream Transcript Variant
CHD1L transcript variant 14 NM_001348458.2:c. N/A Genic Upstream Transcript Variant
CHD1L transcript variant 15 NM_001348459.2:c. N/A Genic Upstream Transcript Variant
CHD1L transcript variant 16 NM_001348460.2:c. N/A Genic Upstream Transcript Variant
CHD1L transcript variant 17 NM_001348461.2:c. N/A Genic Upstream Transcript Variant
CHD1L transcript variant 18 NM_001348462.2:c. N/A Genic Upstream Transcript Variant
CHD1L transcript variant 19 NM_001348463.2:c. N/A Genic Upstream Transcript Variant
CHD1L transcript variant 20 NM_001348464.2:c. N/A Genic Upstream Transcript Variant
CHD1L transcript variant 21 NM_001348465.2:c. N/A Genic Upstream Transcript Variant
CHD1L transcript variant 22 NM_001348466.2:c. N/A Genic Upstream Transcript Variant
CHD1L transcript variant 1 NM_004284.6:c. N/A Genic Upstream Transcript Variant
CHD1L transcript variant 3 NM_024568.4:c. N/A Genic Upstream Transcript Variant
CHD1L transcript variant 6 NR_046070.3:n. N/A Genic Upstream Transcript Variant
CHD1L transcript variant 23 NR_145681.2:n. N/A Genic Upstream Transcript Variant
CHD1L transcript variant 24 NR_145682.2:n. N/A Genic Upstream Transcript Variant
CHD1L transcript variant 25 NR_145683.2:n. N/A Genic Upstream Transcript Variant
CHD1L transcript variant 26 NR_145684.2:n. N/A Genic Upstream Transcript Variant
CHD1L transcript variant 27 NR_145685.2:n. N/A Genic Upstream Transcript Variant
CHD1L transcript variant 28 NR_145686.2:n. N/A Genic Upstream Transcript Variant
CHD1L transcript variant 29 NR_145687.2:n. N/A Genic Upstream Transcript Variant
CHD1L transcript variant 30 NR_145688.2:n. N/A Genic Upstream Transcript Variant
CHD1L transcript variant 31 NR_145689.2:n. N/A Genic Upstream Transcript Variant
CHD1L transcript variant 32 NR_145690.2:n. N/A Genic Upstream Transcript Variant
CHD1L transcript variant 33 NR_145691.2:n. N/A Genic Upstream Transcript Variant
CHD1L transcript variant 34 NR_145692.2:n. N/A Genic Upstream Transcript Variant
CHD1L transcript variant 35 NR_145693.2:n. N/A Genic Upstream Transcript Variant
CHD1L transcript variant 36 NR_145694.2:n. N/A Genic Upstream Transcript Variant
CHD1L transcript variant 37 NR_145695.2:n. N/A Genic Upstream Transcript Variant
CHD1L transcript variant X2 XM_024451051.2:c. N/A Genic Upstream Transcript Variant
CHD1L transcript variant X1 XM_047435001.1: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 1 NC_000001.11:g.147204986= NC_000001.11:g.147204986C>G
GRCh37.p13 chr 1 fix patch HG1287_PATCH NW_003871055.3:g.4020399= NW_003871055.3:g.4020399C>G
CCT8P1 pseudogene NG_016732.3:g.99= NG_016732.3:g.99G>C
CHD1L RefSeqGene NG_052905.1:g.36793= NG_052905.1:g.36793C>G
GRCh37.p13 chr 1 NC_000001.10:g.146676567= NC_000001.10:g.146676567C>G
FMO5 transcript variant X9 XM_006711244.5:c.854= XM_006711244.5:c.854G>C
FMO5 transcript variant X8 XM_006711244.4:c.854= XM_006711244.4:c.854G>C
FMO5 transcript variant X8 XM_006711244.3:c.854= XM_006711244.3:c.854G>C
FMO5 transcript variant X6 XM_006711244.2:c.854= XM_006711244.2:c.854G>C
FMO5 transcript variant X4 XM_006711244.1:c.854= XM_006711244.1:c.854G>C
FMO5 transcript variant X12 XM_047416285.1:c.854= XM_047416285.1:c.854G>C
FMO5 transcript variant X11 XM_047416278.1:c.854= XM_047416278.1:c.854G>C
FMO5 transcript variant X10 XM_047416274.1:c.854= XM_047416274.1:c.854G>C
FMO5 transcript variant X13 XM_047416292.1:c.665= XM_047416292.1:c.665G>C
flavin-containing monooxygenase 5 isoform X3 XP_006711307.1:p.Trp285= XP_006711307.1:p.Trp285Ser
flavin-containing monooxygenase 5 isoform X3 XP_047272241.1:p.Trp285= XP_047272241.1:p.Trp285Ser
flavin-containing monooxygenase 5 isoform X3 XP_047272234.1:p.Trp285= XP_047272234.1:p.Trp285Ser
flavin-containing monooxygenase 5 isoform X3 XP_047272230.1:p.Trp285= XP_047272230.1:p.Trp285Ser
flavin-containing monooxygenase 5 isoform X4 XP_047272248.1:p.Trp222= XP_047272248.1:p.Trp222Ser
FMO5 transcript variant 2 NM_001144829.2:c.831-3481= NM_001144829.2:c.831-3481G>C
FMO5 transcript variant 2 NM_001144829.3:c.831-3482= NM_001144829.3:c.831-3482G>C
FMO5 transcript variant 3 NM_001144830.2:c.830+3847= NM_001144830.2:c.830+3847G>C
FMO5 transcript variant 3 NM_001144830.3:c.830+3866= NM_001144830.3:c.830+3866G>C
CHD1L transcript variant 7 NM_001348451.2:c.-90+30401= NM_001348451.2:c.-90+30401C>G
FMO5 transcript variant 1 NM_001461.3:c.831-3481= NM_001461.3:c.831-3481G>C
FMO5 transcript variant 1 NM_001461.4:c.831-3482= NM_001461.4:c.831-3482G>C
FMO5 transcript variant X1 XM_005272946.1:c.831-3481= XM_005272946.1:c.831-3481G>C
FMO5 transcript variant X1 XM_005272946.6:c.831-3482= XM_005272946.6:c.831-3482G>C
FMO5 transcript variant X2 XM_005272947.1:c.831-3481= XM_005272947.1:c.831-3481G>C
FMO5 transcript variant X4 XM_005272947.6:c.831-3482= XM_005272947.6:c.831-3482G>C
FMO5 transcript variant X3 XM_005272948.1:c.831-3481= XM_005272948.1:c.831-3481G>C
FMO5 transcript variant X3 XM_005272948.6:c.831-3482= XM_005272948.6:c.831-3482G>C
FMO5 transcript variant X4 XM_005272949.1:c.642-3481= XM_005272949.1:c.642-3481G>C
FMO5 transcript variant X5 XM_005272950.1:c.831-3481= XM_005272950.1:c.831-3481G>C
FMO5 transcript variant X1 XM_005277354.1:c.831-3482= XM_005277354.1:c.831-3482G>C
FMO5 transcript variant X2 XM_005277355.1:c.831-3482= XM_005277355.1:c.831-3482G>C
FMO5 transcript variant X3 XM_005277356.1:c.831-3482= XM_005277356.1:c.831-3482G>C
FMO5 transcript variant X4 XM_005277357.1:c.642-3482= XM_005277357.1:c.642-3482G>C
FMO5 transcript variant X5 XM_005277358.1:c.831-3482= XM_005277358.1:c.831-3482G>C
FMO5 transcript variant X2 XM_011509350.4:c.831-3482= XM_011509350.4:c.831-3482G>C
FMO5 transcript variant X5 XM_011509351.4:c.642-3482= XM_011509351.4:c.642-3482G>C
FMO5 transcript variant X7 XM_017000801.3:c.642-3482= XM_017000801.3:c.642-3482G>C
FMO5 transcript variant X8 XM_017000802.3:c.642-3482= XM_017000802.3:c.642-3482G>C
FMO5 transcript variant X6 XM_047416250.1:c.642-3482= XM_047416250.1:c.642-3482G>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 ss4002651811 Apr 25, 2021 (155)
2 TOPMED ss4466669574 Apr 25, 2021 (155)
3 gnomAD - Genomes NC_000001.11 - 147204986 Apr 25, 2021 (155)
4 TopMed NC_000001.11 - 147204986 Apr 25, 2021 (155)
5 ALFA NC_000001.11 - 147204986 Apr 25, 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
25631794, 30275909, 16813962450, ss4002651811, ss4466669574 NC_000001.11:147204985:C:G NC_000001.11:147204985: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 rs1489639613

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