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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.

rs1480100719

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chrY:346209 (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.

This SNP has mapping conflicts. See here for details.

Alleles
T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.000015 (4/264690, TOPMED)
C=0.000014 (2/139826, GnomAD)
C=0.00000 (0/14050, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
PPP2R3B : Missense Variant
LOC124900587 : Missense Variant
LOC124900588 : 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 T=1.00000 C=0.00000 1.0 0.0 0.0 N/A
European Sub 9690 T=1.0000 C=0.0000 1.0 0.0 0.0 N/A
African Sub 2898 T=1.0000 C=0.0000 1.0 0.0 0.0 N/A
African Others Sub 114 T=1.000 C=0.000 1.0 0.0 0.0 N/A
African American Sub 2784 T=1.0000 C=0.0000 1.0 0.0 0.0 N/A
Asian Sub 112 T=1.000 C=0.000 1.0 0.0 0.0 N/A
East Asian Sub 86 T=1.00 C=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 26 T=1.00 C=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 T=1.000 C=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 T=1.000 C=0.000 1.0 0.0 0.0 N/A
South Asian Sub 98 T=1.00 C=0.00 1.0 0.0 0.0 N/A
Other Sub 496 T=1.000 C=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 T=0.999985 C=0.000015
gnomAD - Genomes Global Study-wide 139826 T=0.999986 C=0.000014
gnomAD - Genomes European Sub 75724 T=0.99999 C=0.00001
gnomAD - Genomes African Sub 41862 T=1.00000 C=0.00000
gnomAD - Genomes American Sub 13648 T=1.00000 C=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3322 T=1.0000 C=0.0000
gnomAD - Genomes East Asian Sub 3118 T=0.9997 C=0.0003
gnomAD - Genomes Other Sub 2152 T=1.0000 C=0.0000
Allele Frequency Aggregator Total Global 14050 T=1.00000 C=0.00000
Allele Frequency Aggregator European Sub 9690 T=1.0000 C=0.0000
Allele Frequency Aggregator African Sub 2898 T=1.0000 C=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 T=1.000 C=0.000
Allele Frequency Aggregator Other Sub 496 T=1.000 C=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 T=1.000 C=0.000
Allele Frequency Aggregator Asian Sub 112 T=1.000 C=0.000
Allele Frequency Aggregator South Asian Sub 98 T=1.00 C=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 Y NC_000024.10:g.346209T>C
GRCh37.p13 chr Y NC_000024.9:g.256944T>C
PPP2R3B RefSeqGene NG_013257.1:g.45684A>G
GRCh38.p14 chr X NC_000023.11:g.346209T>C
GRCh37.p13 chr X NC_000023.10:g.306944T>C
GRCh38.p14 chr X alt locus HSCHRX_1_CTG3 NT_187634.1:g.29355T>C
GRCh38.p14 chr X alt locus HSCHRX_2_CTG3 NT_187667.1:g.18729T>C
Gene: PPP2R3B, protein phosphatase 2 regulatory subunit B''beta (minus strand)
Molecule type Change Amino acid[Codon] SO Term
PPP2R3B transcript NM_013239.5:c.844A>G T [ACC] > A [GCC] Coding Sequence Variant
serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta NP_037371.2:p.Thr282Ala T (Thr) > A (Ala) Missense Variant
PPP2R3B transcript variant X2 XM_047442001.1:c.844A>G T [ACC] > A [GCC] Coding Sequence Variant
serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta isoform X1 XP_047297957.1:p.Thr282Ala T (Thr) > A (Ala) Missense Variant
PPP2R3B transcript variant X3 XM_047442002.1:c.760A>G T [ACC] > A [GCC] Coding Sequence Variant
serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta isoform X4 XP_047297958.1:p.Thr254Ala T (Thr) > A (Ala) Missense Variant
PPP2R3B transcript variant X4 XM_011546177.4:c.844A>G T [ACC] > A [GCC] Coding Sequence Variant
serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta isoform X2 XP_011544479.1:p.Thr282Ala T (Thr) > A (Ala) Missense Variant
PPP2R3B transcript variant X5 XM_047442003.1:c.361A>G T [ACC] > A [GCC] Coding Sequence Variant
serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta isoform X3 XP_047297959.1:p.Thr121Ala T (Thr) > A (Ala) Missense Variant
PPP2R3B transcript variant X6 XM_047442004.1:c.361A>G T [ACC] > A [GCC] Coding Sequence Variant
serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta isoform X3 XP_047297960.1:p.Thr121Ala T (Thr) > A (Ala) Missense Variant
PPP2R3B transcript variant X1 XM_047442005.1:c.361A>G T [ACC] > A [GCC] Coding Sequence Variant
serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta isoform X3 XP_047297961.1:p.Thr121Ala T (Thr) > A (Ala) Missense Variant
PPP2R3B transcript variant X7 XM_047442006.1:c.760A>G T [ACC] > A [GCC] Coding Sequence Variant
serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta isoform X5 XP_047297962.1:p.Thr254Ala T (Thr) > A (Ala) 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 T= C
GRCh38.p14 chr Y NC_000024.10:g.346209= NC_000024.10:g.346209T>C
GRCh37.p13 chr Y NC_000024.9:g.256944= NC_000024.9:g.256944T>C
PPP2R3B RefSeqGene NG_013257.1:g.45684= NG_013257.1:g.45684A>G
PPP2R3B transcript NM_013239.5:c.844= NM_013239.5:c.844A>G
PPP2R3B transcript NM_013239.4:c.844= NM_013239.4:c.844A>G
GRCh38.p14 chr X NC_000023.11:g.346209= NC_000023.11:g.346209T>C
GRCh37.p13 chr X NC_000023.10:g.306944= NC_000023.10:g.306944T>C
GRCh38.p14 chr X alt locus HSCHRX_1_CTG3 NT_187634.1:g.29355= NT_187634.1:g.29355T>C
GRCh38.p14 chr X alt locus HSCHRX_2_CTG3 NT_187667.1:g.18729= NT_187667.1:g.18729T>C
PPP2R3B transcript variant X4 XM_011546177.4:c.844= XM_011546177.4:c.844A>G
PPP2R3B transcript variant X1 XM_011546177.3:c.844= XM_011546177.3:c.844A>G
PPP2R3B transcript variant X1 XM_011546177.2:c.844= XM_011546177.2:c.844A>G
PPP2R3B transcript variant X1 XM_011546177.1:c.844= XM_011546177.1:c.844A>G
PPP2R3B transcript variant X4 XM_011545630.4:c.844= XM_011545630.4:c.844A>G
PPP2R3B transcript variant X1 XM_011545630.3:c.844= XM_011545630.3:c.844A>G
PPP2R3B transcript variant X1 XM_011545630.2:c.844= XM_011545630.2:c.844A>G
PPP2R3B transcript variant X1 XM_011545630.1:c.844= XM_011545630.1:c.844A>G
PPP2R3B transcript variant X3 XM_047442002.1:c.760= XM_047442002.1:c.760A>G
PPP2R3B transcript variant X7 XM_047442006.1:c.760= XM_047442006.1:c.760A>G
PPP2R3B transcript variant X2 XM_047442001.1:c.844= XM_047442001.1:c.844A>G
PPP2R3B transcript variant X3 XM_047442724.1:c.760= XM_047442724.1:c.760A>G
PPP2R3B transcript variant X7 XM_047442728.1:c.760= XM_047442728.1:c.760A>G
PPP2R3B transcript variant X1 XM_047442727.1:c.361= XM_047442727.1:c.361A>G
PPP2R3B transcript variant X5 XM_047442725.1:c.361= XM_047442725.1:c.361A>G
PPP2R3B transcript variant X6 XM_047442726.1:c.361= XM_047442726.1:c.361A>G
PPP2R3B transcript variant X2 XM_047442723.1:c.844= XM_047442723.1:c.844A>G
PPP2R3B transcript variant X6 XM_047442004.1:c.361= XM_047442004.1:c.361A>G
PPP2R3B transcript variant X1 XM_047442005.1:c.361= XM_047442005.1:c.361A>G
PPP2R3B transcript variant X5 XM_047442003.1:c.361= XM_047442003.1:c.361A>G
PPP2R3B transcript variant X3 XM_047442954.1:c.760= XM_047442954.1:c.760A>G
PPP2R3B transcript variant X7 XM_047442960.1:c.760= XM_047442960.1:c.760A>G
PPP2R3B transcript variant X4 XM_047442890.1:c.844= XM_047442890.1:c.844A>G
PPP2R3B transcript variant X4 XM_047442956.1:c.844= XM_047442956.1:c.844A>G
PPP2R3B transcript variant X5 XM_047442958.1:c.361= XM_047442958.1:c.361A>G
PPP2R3B transcript variant X2 XM_047442953.1:c.844= XM_047442953.1:c.844A>G
PPP2R3B transcript variant X6 XM_047442959.1:c.361= XM_047442959.1:c.361A>G
PPP2R3B transcript variant X8 XM_047442957.1:c.844= XM_047442957.1:c.844A>G
LOC124900588 transcript variant X1 XM_047442955.1:c.844= XM_047442955.1:c.844A>G
LOC124900587 transcript variant X1 XM_047442889.1:c.844= XM_047442889.1:c.844A>G
serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta NP_037371.2:p.Thr282= NP_037371.2:p.Thr282Ala
serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta isoform X2 XP_011543932.1:p.Thr282= XP_011543932.1:p.Thr282Ala
serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta isoform X4 XP_047298680.1:p.Thr254= XP_047298680.1:p.Thr254Ala
serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta isoform X5 XP_047298684.1:p.Thr254= XP_047298684.1:p.Thr254Ala
serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta isoform X3 XP_047298683.1:p.Thr121= XP_047298683.1:p.Thr121Ala
serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta isoform X3 XP_047298681.1:p.Thr121= XP_047298681.1:p.Thr121Ala
serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta isoform X3 XP_047298682.1:p.Thr121= XP_047298682.1:p.Thr121Ala
serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta isoform X1 XP_047298679.1:p.Thr282= XP_047298679.1:p.Thr282Ala
serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta isoform X2 XP_011544479.1:p.Thr282= XP_011544479.1:p.Thr282Ala
serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta isoform X1 XP_047297957.1:p.Thr282= XP_047297957.1:p.Thr282Ala
serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta isoform X4 XP_047297958.1:p.Thr254= XP_047297958.1:p.Thr254Ala
serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta isoform X3 XP_047297959.1:p.Thr121= XP_047297959.1:p.Thr121Ala
serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta isoform X3 XP_047297960.1:p.Thr121= XP_047297960.1:p.Thr121Ala
serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta isoform X3 XP_047297961.1:p.Thr121= XP_047297961.1:p.Thr121Ala
serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta isoform X5 XP_047297962.1:p.Thr254= XP_047297962.1:p.Thr254Ala
serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta isoform X1 XP_047298845.1:p.Thr282= XP_047298845.1:p.Thr282Ala
serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta isoform X2 XP_047298846.1:p.Thr282= XP_047298846.1:p.Thr282Ala
serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta isoform X1 XP_047298909.1:p.Thr282= XP_047298909.1:p.Thr282Ala
serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta isoform X4 XP_047298910.1:p.Thr254= XP_047298910.1:p.Thr254Ala
serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta isoform X1 XP_047298911.1:p.Thr282= XP_047298911.1:p.Thr282Ala
serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta isoform X2 XP_047298912.1:p.Thr282= XP_047298912.1:p.Thr282Ala
serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta isoform X6 XP_047298913.1:p.Thr282= XP_047298913.1:p.Thr282Ala
serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta isoform X3 XP_047298914.1:p.Thr121= XP_047298914.1:p.Thr121Ala
serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta isoform X3 XP_047298915.1:p.Thr121= XP_047298915.1:p.Thr121Ala
serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta isoform X5 XP_047298916.1:p.Thr254= XP_047298916.1:p.Thr254Ala
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#.

4 SubSNP, 3 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss2746068955 Nov 08, 2017 (151)
2 GNOMAD ss2975768833 Nov 08, 2017 (151)
3 GNOMAD ss4366640133 Apr 27, 2021 (155)
4 TOPMED ss5113336154 Apr 27, 2021 (155)
5 gnomAD - Genomes NC_000023.11 - 346209 Apr 27, 2021 (155)
6 TopMed NC_000023.11 - 346209 Apr 27, 2021 (155)
7 ALFA NC_000024.10 - 346209 Apr 27, 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
ss2746068955, ss2975768833 NC_000023.10:306943:T:C NC_000024.10:346208:T:C (self)
573440390, 676942511, ss4366640133, ss5113336154 NC_000023.11:346208:T:C NC_000024.10:346208:T:C (self)
15123306265 NC_000024.10:346208:T:C NC_000024.10:346208:T:C (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 rs1480100719

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