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dbSNP Short Genetic Variations

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.

rs1487070479

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr10:114203157 (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
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.000004 (1/264690, TOPMED)
G=0.000007 (1/140310, GnomAD)
G=0.00003 (1/35408, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
TDRD1 : 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 35408 A=0.99997 G=0.00003 0.999944 0.0 5.6e-05 0
European Sub 26566 A=0.99996 G=0.00004 0.999925 0.0 0.000075 0
African Sub 2918 A=1.0000 G=0.0000 1.0 0.0 0.0 N/A
African Others Sub 114 A=1.000 G=0.000 1.0 0.0 0.0 N/A
African American Sub 2804 A=1.0000 G=0.0000 1.0 0.0 0.0 N/A
Asian Sub 112 A=1.000 G=0.000 1.0 0.0 0.0 N/A
East Asian Sub 86 A=1.00 G=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 26 A=1.00 G=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 500 A=1.000 G=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 628 A=1.000 G=0.000 1.0 0.0 0.0 N/A
South Asian Sub 98 A=1.00 G=0.00 1.0 0.0 0.0 N/A
Other Sub 4586 A=1.0000 G=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 A=0.999996 G=0.000004
gnomAD - Genomes Global Study-wide 140310 A=0.999993 G=0.000007
gnomAD - Genomes European Sub 75974 A=0.99999 G=0.00001
gnomAD - Genomes African Sub 42068 A=1.00000 G=0.00000
gnomAD - Genomes American Sub 13658 A=1.00000 G=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3324 A=1.0000 G=0.0000
gnomAD - Genomes East Asian Sub 3132 A=1.0000 G=0.0000
gnomAD - Genomes Other Sub 2154 A=1.0000 G=0.0000
Allele Frequency Aggregator Total Global 35408 A=0.99997 G=0.00003
Allele Frequency Aggregator European Sub 26566 A=0.99996 G=0.00004
Allele Frequency Aggregator Other Sub 4586 A=1.0000 G=0.0000
Allele Frequency Aggregator African Sub 2918 A=1.0000 G=0.0000
Allele Frequency Aggregator Latin American 2 Sub 628 A=1.000 G=0.000
Allele Frequency Aggregator Latin American 1 Sub 500 A=1.000 G=0.000
Allele Frequency Aggregator Asian Sub 112 A=1.000 G=0.000
Allele Frequency Aggregator South Asian Sub 98 A=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 10 NC_000010.11:g.114203157A>G
GRCh37.p13 chr 10 NC_000010.10:g.115962916A>G
Gene: TDRD1, tudor domain containing 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
TDRD1 transcript variant 2 NM_001365891.2:c.782A>G K [AAG] > R [AGG] Coding Sequence Variant
tudor domain-containing protein 1 isoform 2 NP_001352820.1:p.Lys261Arg K (Lys) > R (Arg) Missense Variant
TDRD1 transcript variant 10 NM_001385370.1:c.782A>G K [AAG] > R [AGG] Coding Sequence Variant
tudor domain-containing protein 1 isoform 8 NP_001372299.1:p.Lys261Arg K (Lys) > R (Arg) Missense Variant
TDRD1 transcript variant 1 NM_198795.2:c.782A>G K [AAG] > R [AGG] Coding Sequence Variant
tudor domain-containing protein 1 isoform 1 NP_942090.1:p.Lys261Arg K (Lys) > R (Arg) Missense Variant
TDRD1 transcript variant 11 NM_001385371.1:c.782A>G K [AAG] > R [AGG] Coding Sequence Variant
tudor domain-containing protein 1 isoform 9 NP_001372300.1:p.Lys261Arg K (Lys) > R (Arg) Missense Variant
TDRD1 transcript variant 7 NM_001385367.1:c.782A>G K [AAG] > R [AGG] Coding Sequence Variant
tudor domain-containing protein 1 isoform 6 NP_001372296.1:p.Lys261Arg K (Lys) > R (Arg) Missense Variant
TDRD1 transcript variant 6 NM_001385366.1:c.782A>G K [AAG] > R [AGG] Coding Sequence Variant
tudor domain-containing protein 1 isoform 5 NP_001372295.1:p.Lys261Arg K (Lys) > R (Arg) Missense Variant
TDRD1 transcript variant 12 NM_001385372.1:c.782A>G K [AAG] > R [AGG] Coding Sequence Variant
tudor domain-containing protein 1 isoform 10 NP_001372301.1:p.Lys261Arg K (Lys) > R (Arg) Missense Variant
TDRD1 transcript variant 8 NM_001385368.1:c.782A>G K [AAG] > R [AGG] Coding Sequence Variant
tudor domain-containing protein 1 isoform 7 NP_001372297.1:p.Lys261Arg K (Lys) > R (Arg) Missense Variant
TDRD1 transcript variant 3 NM_001385363.1:c.782A>G K [AAG] > R [AGG] Coding Sequence Variant
tudor domain-containing protein 1 isoform 1 NP_001372292.1:p.Lys261Arg K (Lys) > R (Arg) Missense Variant
TDRD1 transcript variant 9 NM_001385369.1:c.782A>G K [AAG] > R [AGG] Coding Sequence Variant
tudor domain-containing protein 1 isoform 7 NP_001372298.1:p.Lys261Arg K (Lys) > R (Arg) Missense Variant
TDRD1 transcript variant 5 NM_001385365.1:c.782A>G K [AAG] > R [AGG] Coding Sequence Variant
tudor domain-containing protein 1 isoform 4 NP_001372294.1:p.Lys261Arg K (Lys) > R (Arg) Missense Variant
TDRD1 transcript variant 4 NM_001385364.2:c.782A>G K [AAG] > R [AGG] Coding Sequence Variant
tudor domain-containing protein 1 isoform 3 NP_001372293.1:p.Lys261Arg K (Lys) > R (Arg) Missense Variant
TDRD1 transcript variant 13 NM_001395205.1:c.782A>G K [AAG] > R [AGG] Coding Sequence Variant
tudor domain-containing protein 1 isoform 3 NP_001382134.1:p.Lys261Arg K (Lys) > R (Arg) Missense Variant
TDRD1 transcript variant X1 XM_011539959.3:c.782A>G K [AAG] > R [AGG] Coding Sequence Variant
tudor domain-containing protein 1 isoform X1 XP_011538261.1:p.Lys261Arg K (Lys) > R (Arg) Missense Variant
TDRD1 transcript variant X2 XM_011539960.3:c.782A>G K [AAG] > R [AGG] Coding Sequence Variant
tudor domain-containing protein 1 isoform X1 XP_011538262.1:p.Lys261Arg K (Lys) > R (Arg) Missense Variant
TDRD1 transcript variant X3 XM_011539961.3:c.782A>G K [AAG] > R [AGG] Coding Sequence Variant
tudor domain-containing protein 1 isoform X1 XP_011538263.1:p.Lys261Arg K (Lys) > R (Arg) Missense Variant
TDRD1 transcript variant X4 XM_011539962.2:c.782A>G K [AAG] > R [AGG] Coding Sequence Variant
tudor domain-containing protein 1 isoform X1 XP_011538264.1:p.Lys261Arg K (Lys) > R (Arg) Missense Variant
TDRD1 transcript variant X5 XM_017016414.3:c.782A>G K [AAG] > R [AGG] Coding Sequence Variant
tudor domain-containing protein 1 isoform X2 XP_016871903.1:p.Lys261Arg K (Lys) > R (Arg) Missense Variant
TDRD1 transcript variant X6 XM_011539964.3:c.782A>G K [AAG] > R [AGG] Coding Sequence Variant
tudor domain-containing protein 1 isoform X3 XP_011538266.1:p.Lys261Arg K (Lys) > R (Arg) Missense Variant
TDRD1 transcript variant X7 XM_047425486.1:c.782A>G K [AAG] > R [AGG] Coding Sequence Variant
tudor domain-containing protein 1 isoform X3 XP_047281442.1:p.Lys261Arg K (Lys) > R (Arg) Missense Variant
TDRD1 transcript variant X8 XM_047425487.1:c.782A>G K [AAG] > R [AGG] Coding Sequence Variant
tudor domain-containing protein 1 isoform X4 XP_047281443.1:p.Lys261Arg K (Lys) > R (Arg) Missense Variant
TDRD1 transcript variant X9 XM_047425488.1:c.782A>G K [AAG] > R [AGG] Coding Sequence Variant
tudor domain-containing protein 1 isoform X5 XP_047281444.1:p.Lys261Arg K (Lys) > R (Arg) Missense Variant
TDRD1 transcript variant X10 XM_047425489.1:c.782A>G K [AAG] > R [AGG] Coding Sequence Variant
tudor domain-containing protein 1 isoform X6 XP_047281445.1:p.Lys261Arg K (Lys) > R (Arg) Missense Variant
TDRD1 transcript variant X11 XM_047425490.1:c.782A>G K [AAG] > R [AGG] Coding Sequence Variant
tudor domain-containing protein 1 isoform X6 XP_047281446.1:p.Lys261Arg K (Lys) > R (Arg) Missense Variant
TDRD1 transcript variant X12 XM_047425491.1:c.782A>G K [AAG] > R [AGG] Coding Sequence Variant
tudor domain-containing protein 1 isoform X7 XP_047281447.1:p.Lys261Arg K (Lys) > R (Arg) Missense Variant
TDRD1 transcript variant X13 XM_047425492.1:c.782A>G K [AAG] > R [AGG] Coding Sequence Variant
tudor domain-containing protein 1 isoform X7 XP_047281448.1:p.Lys261Arg K (Lys) > R (Arg) 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 A= G
GRCh38.p14 chr 10 NC_000010.11:g.114203157= NC_000010.11:g.114203157A>G
GRCh37.p13 chr 10 NC_000010.10:g.115962916= NC_000010.10:g.115962916A>G
TDRD1 transcript variant X1 XM_011539959.3:c.782= XM_011539959.3:c.782A>G
TDRD1 transcript variant X2 XM_011539959.2:c.782= XM_011539959.2:c.782A>G
TDRD1 transcript variant X2 XM_011539959.1:c.782= XM_011539959.1:c.782A>G
TDRD1 transcript variant X2 XM_011539960.3:c.782= XM_011539960.3:c.782A>G
TDRD1 transcript variant X3 XM_011539960.2:c.782= XM_011539960.2:c.782A>G
TDRD1 transcript variant X3 XM_011539960.1:c.782= XM_011539960.1:c.782A>G
TDRD1 transcript variant X3 XM_011539961.3:c.782= XM_011539961.3:c.782A>G
TDRD1 transcript variant X4 XM_011539961.2:c.782= XM_011539961.2:c.782A>G
TDRD1 transcript variant X4 XM_011539961.1:c.782= XM_011539961.1:c.782A>G
TDRD1 transcript variant X5 XM_017016414.3:c.782= XM_017016414.3:c.782A>G
TDRD1 transcript variant X7 XM_017016414.2:c.782= XM_017016414.2:c.782A>G
TDRD1 transcript variant X7 XM_017016414.1:c.782= XM_017016414.1:c.782A>G
TDRD1 transcript variant X6 XM_011539964.3:c.782= XM_011539964.3:c.782A>G
TDRD1 transcript variant X8 XM_011539964.2:c.782= XM_011539964.2:c.782A>G
TDRD1 transcript variant X8 XM_011539964.1:c.782= XM_011539964.1:c.782A>G
TDRD1 transcript variant 1 NM_198795.2:c.782= NM_198795.2:c.782A>G
TDRD1 transcript variant 1 NM_198795.1:c.782= NM_198795.1:c.782A>G
TDRD1 transcript variant 4 NM_001385364.2:c.782= NM_001385364.2:c.782A>G
TDRD1 transcript variant 4 NM_001385364.1:c.782= NM_001385364.1:c.782A>G
TDRD1 transcript variant 2 NM_001365891.2:c.782= NM_001365891.2:c.782A>G
TDRD1 transcript variant 2 NM_001365891.1:c.782= NM_001365891.1:c.782A>G
TDRD1 transcript variant X4 XM_011539962.2:c.782= XM_011539962.2:c.782A>G
TDRD1 transcript variant X5 XM_011539962.1:c.782= XM_011539962.1:c.782A>G
TDRD1 transcript variant 13 NM_001395205.1:c.782= NM_001395205.1:c.782A>G
TDRD1 transcript variant 6 NM_001385366.1:c.782= NM_001385366.1:c.782A>G
TDRD1 transcript variant 9 NM_001385369.1:c.782= NM_001385369.1:c.782A>G
TDRD1 transcript variant 10 NM_001385370.1:c.782= NM_001385370.1:c.782A>G
TDRD1 transcript variant 11 NM_001385371.1:c.782= NM_001385371.1:c.782A>G
TDRD1 transcript variant 3 NM_001385363.1:c.782= NM_001385363.1:c.782A>G
TDRD1 transcript variant 5 NM_001385365.1:c.782= NM_001385365.1:c.782A>G
TDRD1 transcript variant X7 XM_047425486.1:c.782= XM_047425486.1:c.782A>G
TDRD1 transcript variant 8 NM_001385368.1:c.782= NM_001385368.1:c.782A>G
TDRD1 transcript variant 7 NM_001385367.1:c.782= NM_001385367.1:c.782A>G
TDRD1 transcript variant X8 XM_047425487.1:c.782= XM_047425487.1:c.782A>G
TDRD1 transcript variant 12 NM_001385372.1:c.782= NM_001385372.1:c.782A>G
TDRD1 transcript variant X9 XM_047425488.1:c.782= XM_047425488.1:c.782A>G
TDRD1 transcript variant X10 XM_047425489.1:c.782= XM_047425489.1:c.782A>G
TDRD1 transcript variant X11 XM_047425490.1:c.782= XM_047425490.1:c.782A>G
TDRD1 transcript variant X12 XM_047425491.1:c.782= XM_047425491.1:c.782A>G
TDRD1 transcript variant X13 XM_047425492.1:c.782= XM_047425492.1:c.782A>G
tudor domain-containing protein 1 isoform X1 XP_011538261.1:p.Lys261= XP_011538261.1:p.Lys261Arg
tudor domain-containing protein 1 isoform X1 XP_011538262.1:p.Lys261= XP_011538262.1:p.Lys261Arg
tudor domain-containing protein 1 isoform X1 XP_011538263.1:p.Lys261= XP_011538263.1:p.Lys261Arg
tudor domain-containing protein 1 isoform X2 XP_016871903.1:p.Lys261= XP_016871903.1:p.Lys261Arg
tudor domain-containing protein 1 isoform X3 XP_011538266.1:p.Lys261= XP_011538266.1:p.Lys261Arg
tudor domain-containing protein 1 isoform 1 NP_942090.1:p.Lys261= NP_942090.1:p.Lys261Arg
tudor domain-containing protein 1 isoform 3 NP_001372293.1:p.Lys261= NP_001372293.1:p.Lys261Arg
tudor domain-containing protein 1 isoform 2 NP_001352820.1:p.Lys261= NP_001352820.1:p.Lys261Arg
tudor domain-containing protein 1 isoform X1 XP_011538264.1:p.Lys261= XP_011538264.1:p.Lys261Arg
tudor domain-containing protein 1 isoform 3 NP_001382134.1:p.Lys261= NP_001382134.1:p.Lys261Arg
tudor domain-containing protein 1 isoform 5 NP_001372295.1:p.Lys261= NP_001372295.1:p.Lys261Arg
tudor domain-containing protein 1 isoform 7 NP_001372298.1:p.Lys261= NP_001372298.1:p.Lys261Arg
tudor domain-containing protein 1 isoform 8 NP_001372299.1:p.Lys261= NP_001372299.1:p.Lys261Arg
tudor domain-containing protein 1 isoform 9 NP_001372300.1:p.Lys261= NP_001372300.1:p.Lys261Arg
tudor domain-containing protein 1 isoform 1 NP_001372292.1:p.Lys261= NP_001372292.1:p.Lys261Arg
tudor domain-containing protein 1 isoform 4 NP_001372294.1:p.Lys261= NP_001372294.1:p.Lys261Arg
tudor domain-containing protein 1 isoform X3 XP_047281442.1:p.Lys261= XP_047281442.1:p.Lys261Arg
tudor domain-containing protein 1 isoform 7 NP_001372297.1:p.Lys261= NP_001372297.1:p.Lys261Arg
tudor domain-containing protein 1 isoform 6 NP_001372296.1:p.Lys261= NP_001372296.1:p.Lys261Arg
tudor domain-containing protein 1 isoform X4 XP_047281443.1:p.Lys261= XP_047281443.1:p.Lys261Arg
tudor domain-containing protein 1 isoform 10 NP_001372301.1:p.Lys261= NP_001372301.1:p.Lys261Arg
tudor domain-containing protein 1 isoform X5 XP_047281444.1:p.Lys261= XP_047281444.1:p.Lys261Arg
tudor domain-containing protein 1 isoform X6 XP_047281445.1:p.Lys261= XP_047281445.1:p.Lys261Arg
tudor domain-containing protein 1 isoform X6 XP_047281446.1:p.Lys261= XP_047281446.1:p.Lys261Arg
tudor domain-containing protein 1 isoform X7 XP_047281447.1:p.Lys261= XP_047281447.1:p.Lys261Arg
tudor domain-containing protein 1 isoform X7 XP_047281448.1:p.Lys261= XP_047281448.1:p.Lys261Arg
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 ss4226048729 Apr 26, 2021 (155)
2 TOPMED ss4867425361 Apr 26, 2021 (155)
3 gnomAD - Genomes NC_000010.11 - 114203157 Apr 26, 2021 (155)
4 TopMed NC_000010.11 - 114203157 Apr 26, 2021 (155)
5 ALFA NC_000010.11 - 114203157 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
364744498, 82971016, 1612183361, ss4226048729, ss4867425361 NC_000010.11:114203156:A:G NC_000010.11:114203156:A: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 rs1487070479

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