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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.

rs1487783616

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr9:128492750 (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
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000004 (1/264690, TOPMED)
A=0.000004 (1/251474, GnomAD_exome)
A=0.00000 (0/14050, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ODF2 : 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 14050 G=1.00000 A=0.00000 1.0 0.0 0.0 N/A
European Sub 9690 G=1.0000 A=0.0000 1.0 0.0 0.0 N/A
African Sub 2898 G=1.0000 A=0.0000 1.0 0.0 0.0 N/A
African Others Sub 114 G=1.000 A=0.000 1.0 0.0 0.0 N/A
African American Sub 2784 G=1.0000 A=0.0000 1.0 0.0 0.0 N/A
Asian Sub 112 G=1.000 A=0.000 1.0 0.0 0.0 N/A
East Asian Sub 86 G=1.00 A=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 26 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 98 G=1.00 A=0.00 1.0 0.0 0.0 N/A
Other Sub 496 G=1.000 A=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 G=0.999996 A=0.000004
gnomAD - Exomes Global Study-wide 251474 G=0.999996 A=0.000004
gnomAD - Exomes European Sub 135404 G=0.999993 A=0.000007
gnomAD - Exomes Asian Sub 49010 G=1.00000 A=0.00000
gnomAD - Exomes American Sub 34588 G=1.00000 A=0.00000
gnomAD - Exomes African Sub 16254 G=1.00000 A=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10080 G=1.00000 A=0.00000
gnomAD - Exomes Other Sub 6138 G=1.0000 A=0.0000
Allele Frequency Aggregator Total Global 14050 G=1.00000 A=0.00000
Allele Frequency Aggregator European Sub 9690 G=1.0000 A=0.0000
Allele Frequency Aggregator African Sub 2898 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 496 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 112 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 98 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 9 NC_000009.12:g.128492750G>A
GRCh37.p13 chr 9 NC_000009.11:g.131255029G>A
ODF2 RefSeqGene NG_029568.1:g.42596G>A
Gene: ODF2, outer dense fiber of sperm tails 2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
ODF2 transcript variant 1 NM_153435.1:c.1889G>A R [CGC] > H [CAC] Coding Sequence Variant
outer dense fiber protein 2 isoform 1 NP_702913.1:p.Arg630His R (Arg) > H (His) Missense Variant
ODF2 transcript variant 5 NM_153439.1:c.1772G>A R [CGC] > H [CAC] Coding Sequence Variant
outer dense fiber protein 2 isoform 5 NP_702917.1:p.Arg591His R (Arg) > H (His) Missense Variant
ODF2 transcript variant 3 NM_153432.1:c.1829G>A R [CGC] > H [CAC] Coding Sequence Variant
outer dense fiber protein 2 isoform 3 NP_702910.1:p.Arg610His R (Arg) > H (His) Missense Variant
ODF2 transcript variant 12 NM_001351577.1:c.1946G>A R [CGC] > H [CAC] Coding Sequence Variant
outer dense fiber protein 2 isoform 12 NP_001338506.1:p.Arg649His R (Arg) > H (His) Missense Variant
ODF2 transcript variant 16 NM_001351581.1:c.1829G>A R [CGC] > H [CAC] Coding Sequence Variant
outer dense fiber protein 2 isoform 15 NP_001338510.1:p.Arg610His R (Arg) > H (His) Missense Variant
ODF2 transcript variant 20 NM_001351585.2:c.1682G>A R [CGC] > H [CAC] Coding Sequence Variant
outer dense fiber protein 2 isoform 11 NP_001338514.1:p.Arg561His R (Arg) > H (His) Missense Variant
ODF2 transcript variant 18 NM_001351583.2:c.1625G>A R [CGC] > H [CAC] Coding Sequence Variant
outer dense fiber protein 2 isoform 17 NP_001338512.1:p.Arg542His R (Arg) > H (His) Missense Variant
ODF2 transcript variant 17 NM_001351582.2:c.1814G>A R [CGC] > H [CAC] Coding Sequence Variant
outer dense fiber protein 2 isoform 16 NP_001338511.1:p.Arg605His R (Arg) > H (His) Missense Variant
ODF2 transcript variant 9 NM_002540.5:c.1625G>A R [CGC] > H [CAC] Coding Sequence Variant
outer dense fiber protein 2 isoform 9 NP_002531.3:p.Arg542His R (Arg) > H (His) Missense Variant
ODF2 transcript variant 14 NM_001351579.2:c.1682G>A R [CGC] > H [CAC] Coding Sequence Variant
outer dense fiber protein 2 isoform 14 NP_001338508.1:p.Arg561His R (Arg) > H (His) Missense Variant
ODF2 transcript variant 22 NM_001351587.2:c.1511G>A R [CGC] > H [CAC] Coding Sequence Variant
outer dense fiber protein 2 isoform 18 NP_001338516.1:p.Arg504His R (Arg) > H (His) Missense Variant
ODF2 transcript variant 2 NM_153433.2:c.1697G>A R [CGC] > H [CAC] Coding Sequence Variant
outer dense fiber protein 2 isoform 2 NP_702911.1:p.Arg566His R (Arg) > H (His) Missense Variant
ODF2 transcript variant 15 NM_001351580.2:c.1682G>A R [CGC] > H [CAC] Coding Sequence Variant
outer dense fiber protein 2 isoform 14 NP_001338509.1:p.Arg561His R (Arg) > H (His) Missense Variant
ODF2 transcript variant 19 NM_001351584.2:c.1682G>A R [CGC] > H [CAC] Coding Sequence Variant
outer dense fiber protein 2 isoform 11 NP_001338513.1:p.Arg561His R (Arg) > H (His) Missense Variant
ODF2 transcript variant 21 NM_001351586.2:c.1625G>A R [CGC] > H [CAC] Coding Sequence Variant
outer dense fiber protein 2 isoform 9 NP_001338515.1:p.Arg542His R (Arg) > H (His) Missense Variant
ODF2 transcript variant 23 NM_001351588.2:c.1454G>A R [CGC] > H [CAC] Coding Sequence Variant
outer dense fiber protein 2 isoform 19 NP_001338517.1:p.Arg485His R (Arg) > H (His) Missense Variant
ODF2 transcript variant 10 NM_001242353.2:c.1697G>A R [CGC] > H [CAC] Coding Sequence Variant
outer dense fiber protein 2 isoform 2 NP_001229282.1:p.Arg566His R (Arg) > H (His) Missense Variant
ODF2 transcript variant 13 NM_001351578.2:c.1946G>A R [CGC] > H [CAC] Coding Sequence Variant
outer dense fiber protein 2 isoform 13 NP_001338507.1:p.Arg649His R (Arg) > H (His) Missense Variant
ODF2 transcript variant 6 NM_153437.3:c.1640G>A R [CGC] > H [CAC] Coding Sequence Variant
outer dense fiber protein 2 isoform 6 NP_702915.1:p.Arg547His R (Arg) > H (His) Missense Variant
ODF2 transcript variant 8 NM_001242354.2:c.1454G>A R [CGC] > H [CAC] Coding Sequence Variant
outer dense fiber protein 2 isoform 8 NP_001229283.1:p.Arg485His R (Arg) > H (His) Missense Variant
ODF2 transcript variant 4 NM_153436.2:c.1697G>A R [CGC] > H [CAC] Coding Sequence Variant
outer dense fiber protein 2 isoform 4 NP_702914.1:p.Arg566His R (Arg) > H (His) Missense Variant
ODF2 transcript variant 7 NM_153440.2:c.1640G>A R [CGC] > H [CAC] Coding Sequence Variant
outer dense fiber protein 2 isoform 7 NP_702918.1:p.Arg547His R (Arg) > H (His) Missense Variant
ODF2 transcript variant 11 NM_001242352.2:c.1682G>A R [CGC] > H [CAC] Coding Sequence Variant
outer dense fiber protein 2 isoform 11 NP_001229281.1:p.Arg561His R (Arg) > 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
GRCh38.p14 chr 9 NC_000009.12:g.128492750= NC_000009.12:g.128492750G>A
GRCh37.p13 chr 9 NC_000009.11:g.131255029= NC_000009.11:g.131255029G>A
ODF2 RefSeqGene NG_029568.1:g.42596= NG_029568.1:g.42596G>A
ODF2 transcript variant 9 NM_002540.4:c.1625= NM_002540.4:c.1625G>A
ODF2 transcript variant 9 NM_002540.5:c.1625= NM_002540.5:c.1625G>A
ODF2 transcript variant 6 NM_153437.2:c.1640= NM_153437.2:c.1640G>A
ODF2 transcript variant 6 NM_153437.3:c.1640= NM_153437.3:c.1640G>A
ODF2 transcript variant 15 NM_001351580.1:c.1682= NM_001351580.1:c.1682G>A
ODF2 transcript variant 15 NM_001351580.2:c.1682= NM_001351580.2:c.1682G>A
ODF2 transcript variant 20 NM_001351585.1:c.1682= NM_001351585.1:c.1682G>A
ODF2 transcript variant 20 NM_001351585.2:c.1682= NM_001351585.2:c.1682G>A
ODF2 transcript variant 17 NM_001351582.1:c.1814= NM_001351582.1:c.1814G>A
ODF2 transcript variant 17 NM_001351582.2:c.1814= NM_001351582.2:c.1814G>A
ODF2 transcript variant 14 NM_001351579.1:c.1682= NM_001351579.1:c.1682G>A
ODF2 transcript variant 14 NM_001351579.2:c.1682= NM_001351579.2:c.1682G>A
ODF2 transcript variant 12 NM_001351577.1:c.1946= NM_001351577.1:c.1946G>A
ODF2 transcript variant 18 NM_001351583.1:c.1625= NM_001351583.1:c.1625G>A
ODF2 transcript variant 18 NM_001351583.2:c.1625= NM_001351583.2:c.1625G>A
ODF2 transcript variant 10 NM_001242353.1:c.1697= NM_001242353.1:c.1697G>A
ODF2 transcript variant 10 NM_001242353.2:c.1697= NM_001242353.2:c.1697G>A
ODF2 transcript variant 2 NM_153433.1:c.1697= NM_153433.1:c.1697G>A
ODF2 transcript variant 2 NM_153433.2:c.1697= NM_153433.2:c.1697G>A
ODF2 transcript variant 11 NM_001242352.1:c.1682= NM_001242352.1:c.1682G>A
ODF2 transcript variant 11 NM_001242352.2:c.1682= NM_001242352.2:c.1682G>A
ODF2 transcript variant 13 NM_001351578.1:c.1946= NM_001351578.1:c.1946G>A
ODF2 transcript variant 13 NM_001351578.2:c.1946= NM_001351578.2:c.1946G>A
ODF2 transcript variant 21 NM_001351586.1:c.1625= NM_001351586.1:c.1625G>A
ODF2 transcript variant 21 NM_001351586.2:c.1625= NM_001351586.2:c.1625G>A
ODF2 transcript variant 1 NM_153435.1:c.1889= NM_153435.1:c.1889G>A
ODF2 transcript variant 16 NM_001351581.1:c.1829= NM_001351581.1:c.1829G>A
ODF2 transcript variant 22 NM_001351587.1:c.1511= NM_001351587.1:c.1511G>A
ODF2 transcript variant 22 NM_001351587.2:c.1511= NM_001351587.2:c.1511G>A
ODF2 transcript variant 19 NM_001351584.1:c.1682= NM_001351584.1:c.1682G>A
ODF2 transcript variant 19 NM_001351584.2:c.1682= NM_001351584.2:c.1682G>A
ODF2 transcript variant 23 NM_001351588.1:c.1454= NM_001351588.1:c.1454G>A
ODF2 transcript variant 23 NM_001351588.2:c.1454= NM_001351588.2:c.1454G>A
ODF2 transcript variant 3 NM_153432.1:c.1829= NM_153432.1:c.1829G>A
ODF2 transcript variant 8 NM_001242354.1:c.1454= NM_001242354.1:c.1454G>A
ODF2 transcript variant 8 NM_001242354.2:c.1454= NM_001242354.2:c.1454G>A
ODF2 transcript variant 7 NM_153440.1:c.1640= NM_153440.1:c.1640G>A
ODF2 transcript variant 7 NM_153440.2:c.1640= NM_153440.2:c.1640G>A
ODF2 transcript variant 5 NM_153439.1:c.1772= NM_153439.1:c.1772G>A
ODF2 transcript variant 4 NM_153436.1:c.1697= NM_153436.1:c.1697G>A
ODF2 transcript variant 4 NM_153436.2:c.1697= NM_153436.2:c.1697G>A
ODF2 transcript variant 9 NR_036755.1:n.2357= NR_036755.1:n.2357G>A
ODF2 transcript variant 10 NR_036756.1:n.2155= NR_036756.1:n.2155G>A
ODF2 transcript variant 11 NR_036757.1:n.2069= NR_036757.1:n.2069G>A
ODF2 transcript variant 8 NR_036754.1:n.1841= NR_036754.1:n.1841G>A
outer dense fiber protein 2 isoform 9 NP_002531.3:p.Arg542= NP_002531.3:p.Arg542His
outer dense fiber protein 2 isoform 6 NP_702915.1:p.Arg547= NP_702915.1:p.Arg547His
outer dense fiber protein 2 isoform 14 NP_001338509.1:p.Arg561= NP_001338509.1:p.Arg561His
outer dense fiber protein 2 isoform 11 NP_001338514.1:p.Arg561= NP_001338514.1:p.Arg561His
outer dense fiber protein 2 isoform 16 NP_001338511.1:p.Arg605= NP_001338511.1:p.Arg605His
outer dense fiber protein 2 isoform 14 NP_001338508.1:p.Arg561= NP_001338508.1:p.Arg561His
outer dense fiber protein 2 isoform 12 NP_001338506.1:p.Arg649= NP_001338506.1:p.Arg649His
outer dense fiber protein 2 isoform 17 NP_001338512.1:p.Arg542= NP_001338512.1:p.Arg542His
outer dense fiber protein 2 isoform 2 NP_001229282.1:p.Arg566= NP_001229282.1:p.Arg566His
outer dense fiber protein 2 isoform 2 NP_702911.1:p.Arg566= NP_702911.1:p.Arg566His
outer dense fiber protein 2 isoform 11 NP_001229281.1:p.Arg561= NP_001229281.1:p.Arg561His
outer dense fiber protein 2 isoform 13 NP_001338507.1:p.Arg649= NP_001338507.1:p.Arg649His
outer dense fiber protein 2 isoform 9 NP_001338515.1:p.Arg542= NP_001338515.1:p.Arg542His
outer dense fiber protein 2 isoform 1 NP_702913.1:p.Arg630= NP_702913.1:p.Arg630His
outer dense fiber protein 2 isoform 15 NP_001338510.1:p.Arg610= NP_001338510.1:p.Arg610His
outer dense fiber protein 2 isoform 18 NP_001338516.1:p.Arg504= NP_001338516.1:p.Arg504His
outer dense fiber protein 2 isoform 11 NP_001338513.1:p.Arg561= NP_001338513.1:p.Arg561His
outer dense fiber protein 2 isoform 19 NP_001338517.1:p.Arg485= NP_001338517.1:p.Arg485His
outer dense fiber protein 2 isoform 3 NP_702910.1:p.Arg610= NP_702910.1:p.Arg610His
outer dense fiber protein 2 isoform 8 NP_001229283.1:p.Arg485= NP_001229283.1:p.Arg485His
outer dense fiber protein 2 isoform 7 NP_702918.1:p.Arg547= NP_702918.1:p.Arg547His
outer dense fiber protein 2 isoform 5 NP_702917.1:p.Arg591= NP_702917.1:p.Arg591His
outer dense fiber protein 2 isoform 4 NP_702914.1:p.Arg566= NP_702914.1:p.Arg566His
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 ss2737904225 Nov 08, 2017 (151)
2 TOPMED ss4836876555 Apr 26, 2021 (155)
3 gnomAD - Exomes NC_000009.11 - 131255029 Jul 13, 2019 (153)
4 TopMed NC_000009.12 - 128492750 Apr 26, 2021 (155)
5 ALFA NC_000009.12 - 128492750 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
7092989, ss2737904225 NC_000009.11:131255028:G:A NC_000009.12:128492749:G:A (self)
674254116, 142650650, ss4836876555 NC_000009.12:128492749:G:A NC_000009.12:128492749:G:A (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 rs1487783616

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