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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.

rs1480948256

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr19:55186266 (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 (1/250978, GnomAD_exome)
A=0.000007 (1/140166, GnomAD) (+ 1 more)
A=0.00000 (0/10680, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
PTPRH : 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 10680 G=1.00000 A=0.00000 1.0 0.0 0.0 N/A
European Sub 6962 G=1.0000 A=0.0000 1.0 0.0 0.0 N/A
African Sub 2294 G=1.0000 A=0.0000 1.0 0.0 0.0 N/A
African Others Sub 84 G=1.00 A=0.00 1.0 0.0 0.0 N/A
African American Sub 2210 G=1.0000 A=0.0000 1.0 0.0 0.0 N/A
Asian Sub 108 G=1.000 A=0.000 1.0 0.0 0.0 N/A
East Asian Sub 84 G=1.00 A=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 24 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 94 G=1.00 A=0.00 1.0 0.0 0.0 N/A
Other Sub 466 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 250978 G=0.999996 A=0.000004
gnomAD - Exomes European Sub 135038 G=1.000000 A=0.000000
gnomAD - Exomes Asian Sub 48998 G=1.00000 A=0.00000
gnomAD - Exomes American Sub 34560 G=1.00000 A=0.00000
gnomAD - Exomes African Sub 16226 G=0.99994 A=0.00006
gnomAD - Exomes Ashkenazi Jewish Sub 10034 G=1.00000 A=0.00000
gnomAD - Exomes Other Sub 6122 G=1.0000 A=0.0000
gnomAD - Genomes Global Study-wide 140166 G=0.999993 A=0.000007
gnomAD - Genomes European Sub 75926 G=1.00000 A=0.00000
gnomAD - Genomes African Sub 42008 G=0.99998 A=0.00002
gnomAD - Genomes American Sub 13628 G=1.00000 A=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3322 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3128 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2154 G=1.0000 A=0.0000
Allele Frequency Aggregator Total Global 10680 G=1.00000 A=0.00000
Allele Frequency Aggregator European Sub 6962 G=1.0000 A=0.0000
Allele Frequency Aggregator African Sub 2294 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 466 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 108 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 94 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 19 NC_000019.10:g.55186266G>A
GRCh37.p13 chr 19 NC_000019.9:g.55697634G>A
Gene: PTPRH, protein tyrosine phosphatase receptor type H (minus strand)
Molecule type Change Amino acid[Codon] SO Term
PTPRH transcript variant 1 NM_002842.5:c.2737C>T H [CAC] > Y [TAC] Coding Sequence Variant
receptor-type tyrosine-protein phosphatase H isoform 1 precursor NP_002833.4:p.His913Tyr H (His) > Y (Tyr) Missense Variant
PTPRH transcript variant 2 NM_001161440.3:c.2203C>T H [CAC] > Y [TAC] Coding Sequence Variant
receptor-type tyrosine-protein phosphatase H isoform 2 precursor NP_001154912.2:p.His735Tyr H (His) > Y (Tyr) Missense Variant
PTPRH transcript variant X24 XM_011527190.2:c. N/A Genic Downstream Transcript Variant
PTPRH transcript variant X22 XM_017027064.2:c. N/A Genic Downstream Transcript Variant
PTPRH transcript variant X23 XM_047439154.1:c. N/A Genic Downstream Transcript Variant
PTPRH transcript variant X1 XM_017027056.1:c.2803C>T H [CAC] > Y [TAC] Coding Sequence Variant
receptor-type tyrosine-protein phosphatase H isoform X1 XP_016882545.1:p.His935Tyr H (His) > Y (Tyr) Missense Variant
PTPRH transcript variant X2 XM_017027057.1:c.2791C>T H [CAC] > Y [TAC] Coding Sequence Variant
receptor-type tyrosine-protein phosphatase H isoform X2 XP_016882546.1:p.His931Tyr H (His) > Y (Tyr) Missense Variant
PTPRH transcript variant X6 XM_017027059.1:c.2803C>T H [CAC] > Y [TAC] Coding Sequence Variant
receptor-type tyrosine-protein phosphatase H isoform X6 XP_016882548.1:p.His935Tyr H (His) > Y (Tyr) Missense Variant
PTPRH transcript variant X7 XM_017027060.1:c.2755C>T H [CAC] > Y [TAC] Coding Sequence Variant
receptor-type tyrosine-protein phosphatase H isoform X7 XP_016882549.1:p.His919Tyr H (His) > Y (Tyr) Missense Variant
PTPRH transcript variant X15 XM_017027061.1:c.2269C>T H [CAC] > Y [TAC] Coding Sequence Variant
receptor-type tyrosine-protein phosphatase H isoform X15 XP_016882550.1:p.His757Tyr H (His) > Y (Tyr) Missense Variant
PTPRH transcript variant X19 XM_017027063.1:c.2176C>T H [CAC] > Y [TAC] Coding Sequence Variant
receptor-type tyrosine-protein phosphatase H isoform X16 XP_016882552.1:p.His726Tyr H (His) > Y (Tyr) Missense Variant
PTPRH transcript variant X3 XM_017027058.2:c.2782C>T H [CAC] > Y [TAC] Coding Sequence Variant
receptor-type tyrosine-protein phosphatase H isoform X3 XP_016882547.1:p.His928Tyr H (His) > Y (Tyr) Missense Variant
PTPRH transcript variant X4 XM_047439144.1:c.2770C>T H [CAC] > Y [TAC] Coding Sequence Variant
receptor-type tyrosine-protein phosphatase H isoform X4 XP_047295100.1:p.His924Tyr H (His) > Y (Tyr) Missense Variant
PTPRH transcript variant X5 XM_011527183.2:c.2758C>T H [CAC] > Y [TAC] Coding Sequence Variant
receptor-type tyrosine-protein phosphatase H isoform X5 XP_011525485.1:p.His920Tyr H (His) > Y (Tyr) Missense Variant
PTPRH transcript variant X8 XM_047439145.1:c.2791C>T H [CAC] > Y [TAC] Coding Sequence Variant
receptor-type tyrosine-protein phosphatase H isoform X8 XP_047295101.1:p.His931Tyr H (His) > Y (Tyr) Missense Variant
PTPRH transcript variant X9 XM_047439146.1:c.2782C>T H [CAC] > Y [TAC] Coding Sequence Variant
receptor-type tyrosine-protein phosphatase H isoform X9 XP_047295102.1:p.His928Tyr H (His) > Y (Tyr) Missense Variant
PTPRH transcript variant X10 XM_047439147.1:c.2734C>T H [CAC] > Y [TAC] Coding Sequence Variant
receptor-type tyrosine-protein phosphatase H isoform X10 XP_047295103.1:p.His912Tyr H (His) > Y (Tyr) Missense Variant
PTPRH transcript variant X11 XM_047439148.1:c.2725C>T H [CAC] > Y [TAC] Coding Sequence Variant
receptor-type tyrosine-protein phosphatase H isoform X11 XP_047295104.1:p.His909Tyr H (His) > Y (Tyr) Missense Variant
PTPRH transcript variant X12 XM_047439149.1:c.2737C>T H [CAC] > Y [TAC] Coding Sequence Variant
receptor-type tyrosine-protein phosphatase H isoform X12 XP_047295105.1:p.His913Tyr H (His) > Y (Tyr) Missense Variant
PTPRH transcript variant X13 XM_047439150.1:c.2725C>T H [CAC] > Y [TAC] Coding Sequence Variant
receptor-type tyrosine-protein phosphatase H isoform X13 XP_047295106.1:p.His909Tyr H (His) > Y (Tyr) Missense Variant
PTPRH transcript variant X14 XM_047439151.1:c.2803C>T H [CAC] > Y [TAC] Coding Sequence Variant
receptor-type tyrosine-protein phosphatase H isoform X14 XP_047295107.1:p.His935Tyr H (His) > Y (Tyr) Missense Variant
PTPRH transcript variant X16 XM_047439152.1:c.2176C>T H [CAC] > Y [TAC] Coding Sequence Variant
receptor-type tyrosine-protein phosphatase H isoform X16 XP_047295108.1:p.His726Tyr H (His) > Y (Tyr) Missense Variant
PTPRH transcript variant X17 XM_011527188.2:c.2176C>T H [CAC] > Y [TAC] Coding Sequence Variant
receptor-type tyrosine-protein phosphatase H isoform X16 XP_011525490.1:p.His726Tyr H (His) > Y (Tyr) Missense Variant
PTPRH transcript variant X18 XM_017027062.2:c.2176C>T H [CAC] > Y [TAC] Coding Sequence Variant
receptor-type tyrosine-protein phosphatase H isoform X16 XP_016882551.1:p.His726Tyr H (His) > Y (Tyr) Missense Variant
PTPRH transcript variant X20 XM_047439153.1:c.2164C>T H [CAC] > Y [TAC] Coding Sequence Variant
receptor-type tyrosine-protein phosphatase H isoform X17 XP_047295109.1:p.His722Tyr H (His) > Y (Tyr) Missense Variant
PTPRH transcript variant X21 XR_001753731.1:n. N/A Genic Downstream 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
GRCh38.p14 chr 19 NC_000019.10:g.55186266= NC_000019.10:g.55186266G>A
GRCh37.p13 chr 19 NC_000019.9:g.55697634= NC_000019.9:g.55697634G>A
PTPRH transcript variant 1 NM_002842.5:c.2737= NM_002842.5:c.2737C>T
PTPRH transcript variant 1 NM_002842.4:c.2737= NM_002842.4:c.2737C>T
PTPRH transcript variant 1 NM_002842.3:c.2737= NM_002842.3:c.2737C>T
PTPRH transcript variant 2 NM_001161440.3:c.2203= NM_001161440.3:c.2203C>T
PTPRH transcript variant 2 NM_001161440.2:c.2203= NM_001161440.2:c.2203C>T
PTPRH transcript variant 2 NM_001161440.1:c.2203= NM_001161440.1:c.2203C>T
PTPRH transcript variant X3 XM_017027058.2:c.2782= XM_017027058.2:c.2782C>T
PTPRH transcript variant X3 XM_017027058.1:c.2782= XM_017027058.1:c.2782C>T
PTPRH transcript variant X5 XM_011527183.2:c.2758= XM_011527183.2:c.2758C>T
PTPRH transcript variant X4 XM_011527183.1:c.2758= XM_011527183.1:c.2758C>T
PTPRH transcript variant X17 XM_011527188.2:c.2176= XM_011527188.2:c.2176C>T
PTPRH transcript variant X9 XM_011527188.1:c.2176= XM_011527188.1:c.2176C>T
PTPRH transcript variant X18 XM_017027062.2:c.2176= XM_017027062.2:c.2176C>T
PTPRH transcript variant X10 XM_017027062.1:c.2176= XM_017027062.1:c.2176C>T
PTPRH transcript variant X1 XM_017027056.1:c.2803= XM_017027056.1:c.2803C>T
PTPRH transcript variant X2 XM_017027057.1:c.2791= XM_017027057.1:c.2791C>T
PTPRH transcript variant X11 XM_047439148.1:c.2725= XM_047439148.1:c.2725C>T
PTPRH transcript variant X4 XM_047439144.1:c.2770= XM_047439144.1:c.2770C>T
PTPRH transcript variant X16 XM_047439152.1:c.2176= XM_047439152.1:c.2176C>T
PTPRH transcript variant X7 XM_017027060.1:c.2755= XM_017027060.1:c.2755C>T
PTPRH transcript variant X6 XM_017027059.1:c.2803= XM_017027059.1:c.2803C>T
PTPRH transcript variant X20 XM_047439153.1:c.2164= XM_047439153.1:c.2164C>T
PTPRH transcript variant X8 XM_047439145.1:c.2791= XM_047439145.1:c.2791C>T
PTPRH transcript variant X12 XM_047439149.1:c.2737= XM_047439149.1:c.2737C>T
PTPRH transcript variant X10 XM_047439147.1:c.2734= XM_047439147.1:c.2734C>T
PTPRH transcript variant X9 XM_047439146.1:c.2782= XM_047439146.1:c.2782C>T
PTPRH transcript variant X13 XM_047439150.1:c.2725= XM_047439150.1:c.2725C>T
PTPRH transcript variant X19 XM_017027063.1:c.2176= XM_017027063.1:c.2176C>T
PTPRH transcript variant X15 XM_017027061.1:c.2269= XM_017027061.1:c.2269C>T
PTPRH transcript variant X14 XM_047439151.1:c.2803= XM_047439151.1:c.2803C>T
receptor-type tyrosine-protein phosphatase H isoform 1 precursor NP_002833.4:p.His913= NP_002833.4:p.His913Tyr
receptor-type tyrosine-protein phosphatase H isoform 2 precursor NP_001154912.2:p.His735= NP_001154912.2:p.His735Tyr
receptor-type tyrosine-protein phosphatase H isoform X3 XP_016882547.1:p.His928= XP_016882547.1:p.His928Tyr
receptor-type tyrosine-protein phosphatase H isoform X5 XP_011525485.1:p.His920= XP_011525485.1:p.His920Tyr
receptor-type tyrosine-protein phosphatase H isoform X16 XP_011525490.1:p.His726= XP_011525490.1:p.His726Tyr
receptor-type tyrosine-protein phosphatase H isoform X16 XP_016882551.1:p.His726= XP_016882551.1:p.His726Tyr
receptor-type tyrosine-protein phosphatase H isoform X1 XP_016882545.1:p.His935= XP_016882545.1:p.His935Tyr
receptor-type tyrosine-protein phosphatase H isoform X2 XP_016882546.1:p.His931= XP_016882546.1:p.His931Tyr
receptor-type tyrosine-protein phosphatase H isoform X11 XP_047295104.1:p.His909= XP_047295104.1:p.His909Tyr
receptor-type tyrosine-protein phosphatase H isoform X4 XP_047295100.1:p.His924= XP_047295100.1:p.His924Tyr
receptor-type tyrosine-protein phosphatase H isoform X16 XP_047295108.1:p.His726= XP_047295108.1:p.His726Tyr
receptor-type tyrosine-protein phosphatase H isoform X7 XP_016882549.1:p.His919= XP_016882549.1:p.His919Tyr
receptor-type tyrosine-protein phosphatase H isoform X6 XP_016882548.1:p.His935= XP_016882548.1:p.His935Tyr
receptor-type tyrosine-protein phosphatase H isoform X17 XP_047295109.1:p.His722= XP_047295109.1:p.His722Tyr
receptor-type tyrosine-protein phosphatase H isoform X8 XP_047295101.1:p.His931= XP_047295101.1:p.His931Tyr
receptor-type tyrosine-protein phosphatase H isoform X12 XP_047295105.1:p.His913= XP_047295105.1:p.His913Tyr
receptor-type tyrosine-protein phosphatase H isoform X10 XP_047295103.1:p.His912= XP_047295103.1:p.His912Tyr
receptor-type tyrosine-protein phosphatase H isoform X9 XP_047295102.1:p.His928= XP_047295102.1:p.His928Tyr
receptor-type tyrosine-protein phosphatase H isoform X13 XP_047295106.1:p.His909= XP_047295106.1:p.His909Tyr
receptor-type tyrosine-protein phosphatase H isoform X16 XP_016882552.1:p.His726= XP_016882552.1:p.His726Tyr
receptor-type tyrosine-protein phosphatase H isoform X15 XP_016882550.1:p.His757= XP_016882550.1:p.His757Tyr
receptor-type tyrosine-protein phosphatase H isoform X14 XP_047295107.1:p.His935= XP_047295107.1:p.His935Tyr
receptor-type tyrosine-protein phosphatase H isoform 2 precursor NP_001154912.1:p.His735= NP_001154912.1:p.His735Tyr
receptor-type tyrosine-protein phosphatase H isoform 1 precursor NP_002833.3:p.His913= NP_002833.3:p.His913Tyr
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#.

3 SubSNP, 4 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss2744328312 Nov 08, 2017 (151)
2 GNOMAD ss4333341689 Apr 27, 2021 (155)
3 TOPMED ss5078814517 Apr 27, 2021 (155)
4 gnomAD - Genomes NC_000019.10 - 55186266 Apr 27, 2021 (155)
5 gnomAD - Exomes NC_000019.9 - 55697634 Jul 13, 2019 (153)
6 TopMed NC_000019.10 - 55186266 Apr 27, 2021 (155)
7 ALFA NC_000019.10 - 55186266 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
13645186, ss2744328312 NC_000019.9:55697633:G:A NC_000019.10:55186265:G:A (self)
543571904, 294360181, 7365236146, ss4333341689, ss5078814517 NC_000019.10:55186265:G:A NC_000019.10:55186265: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 rs1480948256

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