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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.

rs1486900924

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr16:89716751 (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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000009 (2/230646, GnomAD_exome)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
VPS9D1 : Stop Gained
VPS9D1-AS1 : Non Coding Transcript Variant
Publications
0 citations
Genomic View
See rs on genome
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
gnomAD - Exomes Global Study-wide 230646 G=0.999991 T=0.000009
gnomAD - Exomes European Sub 127516 G=0.999992 T=0.000008
gnomAD - Exomes Asian Sub 45492 G=1.00000 T=0.00000
gnomAD - Exomes American Sub 28452 G=0.99996 T=0.00004
gnomAD - Exomes African Sub 14954 G=1.00000 T=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 8730 G=1.0000 T=0.0000
gnomAD - Exomes Other Sub 5502 G=1.0000 T=0.0000
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 16 NC_000016.10:g.89716751G>A
GRCh38.p14 chr 16 NC_000016.10:g.89716751G>T
GRCh37.p13 chr 16 NC_000016.9:g.89783159G>A
GRCh37.p13 chr 16 NC_000016.9:g.89783159G>T
Gene: VPS9D1, VPS9 domain containing 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
VPS9D1 transcript NM_004913.3:c.247C>T Q [CAG] > * [TAG] Coding Sequence Variant
VPS9 domain-containing protein 1 NP_004904.2:p.Gln83Ter Q (Gln) > * (Ter) Stop Gained
VPS9D1 transcript NM_004913.3:c.247C>A Q [CAG] > K [AAG] Coding Sequence Variant
VPS9 domain-containing protein 1 NP_004904.2:p.Gln83Lys Q (Gln) > K (Lys) Missense Variant
VPS9D1 transcript variant X1 XM_047434930.1:c.247C>T Q [CAG] > * [TAG] Coding Sequence Variant
VPS9 domain-containing protein 1 isoform X1 XP_047290886.1:p.Gln83Ter Q (Gln) > * (Ter) Stop Gained
VPS9D1 transcript variant X1 XM_047434930.1:c.247C>A Q [CAG] > K [AAG] Coding Sequence Variant
VPS9 domain-containing protein 1 isoform X1 XP_047290886.1:p.Gln83Lys Q (Gln) > K (Lys) Missense Variant
VPS9D1 transcript variant X2 XM_047434931.1:c.244C>T Q [CAG] > * [TAG] Coding Sequence Variant
VPS9 domain-containing protein 1 isoform X2 XP_047290887.1:p.Gln82Ter Q (Gln) > * (Ter) Stop Gained
VPS9D1 transcript variant X2 XM_047434931.1:c.244C>A Q [CAG] > K [AAG] Coding Sequence Variant
VPS9 domain-containing protein 1 isoform X2 XP_047290887.1:p.Gln82Lys Q (Gln) > K (Lys) Missense Variant
VPS9D1 transcript variant X3 XM_005256329.6:c.247C>T Q [CAG] > * [TAG] Coding Sequence Variant
VPS9 domain-containing protein 1 isoform X3 XP_005256386.1:p.Gln83Ter Q (Gln) > * (Ter) Stop Gained
VPS9D1 transcript variant X3 XM_005256329.6:c.247C>A Q [CAG] > K [AAG] Coding Sequence Variant
VPS9 domain-containing protein 1 isoform X3 XP_005256386.1:p.Gln83Lys Q (Gln) > K (Lys) Missense Variant
VPS9D1 transcript variant X4 XM_011523476.4:c.244C>T Q [CAG] > * [TAG] Coding Sequence Variant
VPS9 domain-containing protein 1 isoform X4 XP_011521778.1:p.Gln82Ter Q (Gln) > * (Ter) Stop Gained
VPS9D1 transcript variant X4 XM_011523476.4:c.244C>A Q [CAG] > K [AAG] Coding Sequence Variant
VPS9 domain-containing protein 1 isoform X4 XP_011521778.1:p.Gln82Lys Q (Gln) > K (Lys) Missense Variant
VPS9D1 transcript variant X5 XM_047434932.1:c.244C>T Q [CAG] > * [TAG] Coding Sequence Variant
VPS9 domain-containing protein 1 isoform X5 XP_047290888.1:p.Gln82Ter Q (Gln) > * (Ter) Stop Gained
VPS9D1 transcript variant X5 XM_047434932.1:c.244C>A Q [CAG] > K [AAG] Coding Sequence Variant
VPS9 domain-containing protein 1 isoform X5 XP_047290888.1:p.Gln82Lys Q (Gln) > K (Lys) Missense Variant
VPS9D1 transcript variant X6 XM_047434933.1:c.145C>T Q [CAG] > * [TAG] Coding Sequence Variant
VPS9 domain-containing protein 1 isoform X6 XP_047290889.1:p.Gln49Ter Q (Gln) > * (Ter) Stop Gained
VPS9D1 transcript variant X6 XM_047434933.1:c.145C>A Q [CAG] > K [AAG] Coding Sequence Variant
VPS9 domain-containing protein 1 isoform X6 XP_047290889.1:p.Gln49Lys Q (Gln) > K (Lys) Missense Variant
VPS9D1 transcript variant X7 XM_047434934.1:c.142C>T Q [CAG] > * [TAG] Coding Sequence Variant
VPS9 domain-containing protein 1 isoform X7 XP_047290890.1:p.Gln48Ter Q (Gln) > * (Ter) Stop Gained
VPS9D1 transcript variant X7 XM_047434934.1:c.142C>A Q [CAG] > K [AAG] Coding Sequence Variant
VPS9 domain-containing protein 1 isoform X7 XP_047290890.1:p.Gln48Lys Q (Gln) > K (Lys) Missense Variant
VPS9D1 transcript variant X8 XM_047434935.1:c.247C>T Q [CAG] > * [TAG] Coding Sequence Variant
VPS9 domain-containing protein 1 isoform X8 XP_047290891.1:p.Gln83Ter Q (Gln) > * (Ter) Stop Gained
VPS9D1 transcript variant X8 XM_047434935.1:c.247C>A Q [CAG] > K [AAG] Coding Sequence Variant
VPS9 domain-containing protein 1 isoform X8 XP_047290891.1:p.Gln83Lys Q (Gln) > K (Lys) Missense Variant
VPS9D1 transcript variant X9 XM_047434936.1:c.247C>T Q [CAG] > * [TAG] Coding Sequence Variant
VPS9 domain-containing protein 1 isoform X9 XP_047290892.1:p.Gln83Ter Q (Gln) > * (Ter) Stop Gained
VPS9D1 transcript variant X9 XM_047434936.1:c.247C>A Q [CAG] > K [AAG] Coding Sequence Variant
VPS9 domain-containing protein 1 isoform X9 XP_047290892.1:p.Gln83Lys Q (Gln) > K (Lys) Missense Variant
VPS9D1 transcript variant X10 XM_047434937.1:c.37C>T Q [CAG] > * [TAG] Coding Sequence Variant
VPS9 domain-containing protein 1 isoform X10 XP_047290893.1:p.Gln13Ter Q (Gln) > * (Ter) Stop Gained
VPS9D1 transcript variant X10 XM_047434937.1:c.37C>A Q [CAG] > K [AAG] Coding Sequence Variant
VPS9 domain-containing protein 1 isoform X10 XP_047290893.1:p.Gln13Lys Q (Gln) > K (Lys) Missense Variant
Gene: VPS9D1-AS1, VPS9D1 antisense RNA 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
VPS9D1-AS1 transcript NR_036480.1:n.778G>A N/A Non Coding Transcript Variant
VPS9D1-AS1 transcript NR_036480.1:n.778G>T 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 T
GRCh38.p14 chr 16 NC_000016.10:g.89716751= NC_000016.10:g.89716751G>A NC_000016.10:g.89716751G>T
GRCh37.p13 chr 16 NC_000016.9:g.89783159= NC_000016.9:g.89783159G>A NC_000016.9:g.89783159G>T
VPS9D1 transcript variant X3 XM_005256329.6:c.247= XM_005256329.6:c.247C>T XM_005256329.6:c.247C>A
VPS9D1 transcript variant X1 XM_005256329.5:c.247= XM_005256329.5:c.247C>T XM_005256329.5:c.247C>A
VPS9D1 transcript variant X1 XM_005256329.4:c.247= XM_005256329.4:c.247C>T XM_005256329.4:c.247C>A
VPS9D1 transcript variant X1 XM_005256329.3:c.247= XM_005256329.3:c.247C>T XM_005256329.3:c.247C>A
VPS9D1 transcript variant X1 XM_005256329.2:c.247= XM_005256329.2:c.247C>T XM_005256329.2:c.247C>A
VPS9D1 transcript variant X1 XM_005256329.1:c.247= XM_005256329.1:c.247C>T XM_005256329.1:c.247C>A
VPS9D1 transcript variant X4 XM_011523476.4:c.244= XM_011523476.4:c.244C>T XM_011523476.4:c.244C>A
VPS9D1 transcript variant X2 XM_011523476.3:c.244= XM_011523476.3:c.244C>T XM_011523476.3:c.244C>A
VPS9D1 transcript variant X2 XM_011523476.2:c.244= XM_011523476.2:c.244C>T XM_011523476.2:c.244C>A
VPS9D1 transcript variant X2 XM_011523476.1:c.244= XM_011523476.1:c.244C>T XM_011523476.1:c.244C>A
VPS9D1 transcript NM_004913.3:c.247= NM_004913.3:c.247C>T NM_004913.3:c.247C>A
VPS9D1 transcript NM_004913.2:c.247= NM_004913.2:c.247C>T NM_004913.2:c.247C>A
VPS9D1 transcript variant X10 XM_047434937.1:c.37= XM_047434937.1:c.37C>T XM_047434937.1:c.37C>A
VPS9D1 transcript variant X1 XM_047434930.1:c.247= XM_047434930.1:c.247C>T XM_047434930.1:c.247C>A
VPS9D1 transcript variant X2 XM_047434931.1:c.244= XM_047434931.1:c.244C>T XM_047434931.1:c.244C>A
VPS9D1 transcript variant X5 XM_047434932.1:c.244= XM_047434932.1:c.244C>T XM_047434932.1:c.244C>A
VPS9D1 transcript variant X8 XM_047434935.1:c.247= XM_047434935.1:c.247C>T XM_047434935.1:c.247C>A
VPS9D1 transcript variant X6 XM_047434933.1:c.145= XM_047434933.1:c.145C>T XM_047434933.1:c.145C>A
VPS9D1 transcript variant X7 XM_047434934.1:c.142= XM_047434934.1:c.142C>T XM_047434934.1:c.142C>A
VPS9D1 transcript variant X9 XM_047434936.1:c.247= XM_047434936.1:c.247C>T XM_047434936.1:c.247C>A
VPS9D1-AS1 transcript NR_036480.1:n.778= NR_036480.1:n.778G>A NR_036480.1:n.778G>T
VPS9 domain-containing protein 1 isoform X3 XP_005256386.1:p.Gln83= XP_005256386.1:p.Gln83Ter XP_005256386.1:p.Gln83Lys
VPS9 domain-containing protein 1 isoform X4 XP_011521778.1:p.Gln82= XP_011521778.1:p.Gln82Ter XP_011521778.1:p.Gln82Lys
VPS9 domain-containing protein 1 NP_004904.2:p.Gln83= NP_004904.2:p.Gln83Ter NP_004904.2:p.Gln83Lys
VPS9 domain-containing protein 1 isoform X10 XP_047290893.1:p.Gln13= XP_047290893.1:p.Gln13Ter XP_047290893.1:p.Gln13Lys
VPS9 domain-containing protein 1 isoform X1 XP_047290886.1:p.Gln83= XP_047290886.1:p.Gln83Ter XP_047290886.1:p.Gln83Lys
VPS9 domain-containing protein 1 isoform X2 XP_047290887.1:p.Gln82= XP_047290887.1:p.Gln82Ter XP_047290887.1:p.Gln82Lys
VPS9 domain-containing protein 1 isoform X5 XP_047290888.1:p.Gln82= XP_047290888.1:p.Gln82Ter XP_047290888.1:p.Gln82Lys
VPS9 domain-containing protein 1 isoform X8 XP_047290891.1:p.Gln83= XP_047290891.1:p.Gln83Ter XP_047290891.1:p.Gln83Lys
VPS9 domain-containing protein 1 isoform X6 XP_047290889.1:p.Gln49= XP_047290889.1:p.Gln49Ter XP_047290889.1:p.Gln49Lys
VPS9 domain-containing protein 1 isoform X7 XP_047290890.1:p.Gln48= XP_047290890.1:p.Gln48Ter XP_047290890.1:p.Gln48Lys
VPS9 domain-containing protein 1 isoform X9 XP_047290892.1:p.Gln83= XP_047290892.1:p.Gln83Ter XP_047290892.1:p.Gln83Lys
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, 1 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss2742263007 Nov 08, 2017 (151)
2 EVA ss5848435069 Oct 17, 2022 (156)
3 gnomAD - Exomes NC_000016.9 - 89783159 Jul 13, 2019 (153)
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
ss5848435069 NC_000016.9:89783158:G:A NC_000016.10:89716750:G:A
11554949, ss2742263007 NC_000016.9:89783158:G:T NC_000016.10:89716750:G:T (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 rs1486900924

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