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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.

rs35947132

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr10:70600631 (GRCh38.p13) 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
A=0.029140 (7713/264690, TOPMED)
A=0.029318 (7315/249508, GnomAD_exome)
A=0.040497 (7686/189792, ALFA) (+ 15 more)
A=0.031059 (3677/118388, ExAC)
A=0.0132 (66/5008, 1000G)
A=0.0397 (178/4480, Estonian)
A=0.0413 (159/3854, ALSPAC)
A=0.0345 (128/3708, TWINSUK)
A=0.059 (59/998, GoNL)
A=0.042 (25/600, NorthernSweden)
A=0.015 (8/534, MGP)
A=0.051 (15/296, FINRISK)
A=0.014 (3/216, Qatari)
A=0.05 (2/40, GENOME_DK)
G=0.50 (9/18, SGDP_PRJ)
A=0.50 (9/18, SGDP_PRJ)
G=0.5 (2/4, Siberian)
A=0.5 (2/4, Siberian)
Clinical Significance
Reported in ClinVar
Gene : Consequence
PRF1 : Missense Variant
Publications
14 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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 189792 G=0.959503 A=0.040497, T=0.000000
European Sub 166390 G=0.957527 A=0.042473, T=0.000000
African Sub 4456 G=0.9951 A=0.0049, T=0.0000
African Others Sub 176 G=1.000 A=0.000, T=0.000
African American Sub 4280 G=0.9949 A=0.0051, T=0.0000
Asian Sub 3338 G=0.9997 A=0.0003, T=0.0000
East Asian Sub 2658 G=0.9996 A=0.0004, T=0.0000
Other Asian Sub 680 G=1.000 A=0.000, T=0.000
Latin American 1 Sub 782 G=0.973 A=0.027, T=0.000
Latin American 2 Sub 934 G=0.990 A=0.010, T=0.000
South Asian Sub 274 G=1.000 A=0.000, T=0.000
Other Sub 13618 G=0.95844 A=0.04156, T=0.00000


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=0.970860 A=0.029140
gnomAD - Exomes Global Study-wide 249508 G=0.970682 A=0.029318
gnomAD - Exomes European Sub 133972 G=0.956648 A=0.043352
gnomAD - Exomes Asian Sub 48940 G=0.99724 A=0.00276
gnomAD - Exomes American Sub 34472 G=0.97697 A=0.02303
gnomAD - Exomes African Sub 16028 G=0.99426 A=0.00574
gnomAD - Exomes Ashkenazi Jewish Sub 10008 G=0.97332 A=0.02668
gnomAD - Exomes Other Sub 6088 G=0.9640 A=0.0360
Allele Frequency Aggregator Total Global 189792 G=0.959503 A=0.040497, T=0.000000
Allele Frequency Aggregator European Sub 166390 G=0.957527 A=0.042473, T=0.000000
Allele Frequency Aggregator Other Sub 13618 G=0.95844 A=0.04156, T=0.00000
Allele Frequency Aggregator African Sub 4456 G=0.9951 A=0.0049, T=0.0000
Allele Frequency Aggregator Asian Sub 3338 G=0.9997 A=0.0003, T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 934 G=0.990 A=0.010, T=0.000
Allele Frequency Aggregator Latin American 1 Sub 782 G=0.973 A=0.027, T=0.000
Allele Frequency Aggregator South Asian Sub 274 G=1.000 A=0.000, T=0.000
ExAC Global Study-wide 118388 G=0.968941 A=0.031059
ExAC Europe Sub 71260 G=0.95394 A=0.04606
ExAC Asian Sub 24952 G=0.99744 A=0.00256
ExAC American Sub 11372 G=0.97819 A=0.02181
ExAC African Sub 9946 G=0.9941 A=0.0059
ExAC Other Sub 858 G=0.972 A=0.028
1000Genomes Global Study-wide 5008 G=0.9868 A=0.0132
1000Genomes African Sub 1322 G=0.9985 A=0.0015
1000Genomes East Asian Sub 1008 G=0.9990 A=0.0010
1000Genomes Europe Sub 1006 G=0.9543 A=0.0457
1000Genomes South Asian Sub 978 G=0.998 A=0.002
1000Genomes American Sub 694 G=0.978 A=0.022
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.9603 A=0.0397
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.9587 A=0.0413
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.9655 A=0.0345
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.941 A=0.059
Northern Sweden ACPOP Study-wide 600 G=0.958 A=0.042
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 G=0.985 A=0.015
FINRISK Finnish from FINRISK project Study-wide 296 G=0.949 A=0.051
Qatari Global Study-wide 216 G=0.986 A=0.014
The Danish reference pan genome Danish Study-wide 40 G=0.95 A=0.05
SGDP_PRJ Global Study-wide 18 G=0.50 A=0.50
Siberian Global Study-wide 4 G=0.5 A=0.5
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.p13 chr 10 NC_000010.11:g.70600631G>A
GRCh38.p13 chr 10 NC_000010.11:g.70600631G>T
GRCh37.p13 chr 10 NC_000010.10:g.72360387G>A
GRCh37.p13 chr 10 NC_000010.10:g.72360387G>T
PRF1 RefSeqGene (LRG_94) NG_009615.1:g.7145C>T
PRF1 RefSeqGene (LRG_94) NG_009615.1:g.7145C>A
Gene: PRF1, perforin 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
PRF1 transcript variant 2 NM_001083116.3:c.272C>T A [GCG] > V [GTG] Coding Sequence Variant
perforin-1 precursor NP_001076585.1:p.Ala91Val A (Ala) > V (Val) Missense Variant
PRF1 transcript variant 2 NM_001083116.3:c.272C>A A [GCG] > E [GAG] Coding Sequence Variant
perforin-1 precursor NP_001076585.1:p.Ala91Glu A (Ala) > E (Glu) Missense Variant
PRF1 transcript variant 1 NM_005041.6:c.272C>T A [GCG] > V [GTG] Coding Sequence Variant
perforin-1 precursor NP_005032.2:p.Ala91Val A (Ala) > V (Val) Missense Variant
PRF1 transcript variant 1 NM_005041.6:c.272C>A A [GCG] > E [GAG] Coding Sequence Variant
perforin-1 precursor NP_005032.2:p.Ala91Glu A (Ala) > E (Glu) 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.

Allele: A (allele ID: 28757 )
ClinVar Accession Disease Names Clinical Significance
RCV000014719.5 Hemophagocytic lymphohistiocytosis, familial, 2, susceptibility to Uncertain-Significance
RCV000224458.1 not provided Conflicting-Interpretations-Of-Pathogenicity
RCV000456018.2 not specified Benign
RCV000547554.4 Familial hemophagocytic lymphohistiocytosis 2 Benign-Likely-Benign
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.p13 chr 10 NC_000010.11:g.70600631= NC_000010.11:g.70600631G>A NC_000010.11:g.70600631G>T
GRCh37.p13 chr 10 NC_000010.10:g.72360387= NC_000010.10:g.72360387G>A NC_000010.10:g.72360387G>T
PRF1 RefSeqGene (LRG_94) NG_009615.1:g.7145= NG_009615.1:g.7145C>T NG_009615.1:g.7145C>A
PRF1 transcript variant 1 NM_005041.6:c.272= NM_005041.6:c.272C>T NM_005041.6:c.272C>A
PRF1 transcript variant 1 NM_005041.5:c.272= NM_005041.5:c.272C>T NM_005041.5:c.272C>A
PRF1 transcript variant 1 NM_005041.4:c.272= NM_005041.4:c.272C>T NM_005041.4:c.272C>A
PRF1 transcript variant 2 NM_001083116.3:c.272= NM_001083116.3:c.272C>T NM_001083116.3:c.272C>A
PRF1 transcript variant 2 NM_001083116.2:c.272= NM_001083116.2:c.272C>T NM_001083116.2:c.272C>A
PRF1 transcript variant 2 NM_001083116.1:c.272= NM_001083116.1:c.272C>T NM_001083116.1:c.272C>A
perforin-1 precursor NP_005032.2:p.Ala91= NP_005032.2:p.Ala91Val NP_005032.2:p.Ala91Glu
perforin-1 precursor NP_001076585.1:p.Ala91= NP_001076585.1:p.Ala91Val NP_001076585.1:p.Ala91Glu
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#.

63 SubSNP, 18 Frequency, 4 ClinVar submissions
No Submitter Submission ID Date (Build)
1 APPLERA_GI ss48420743 Mar 15, 2006 (126)
2 SI_EXO ss52058312 Oct 13, 2006 (127)
3 PERLEGEN ss69082996 May 16, 2007 (127)
4 BCM-HGSC-SUB ss207405928 Jul 04, 2010 (132)
5 1000GENOMES ss235229278 Jul 15, 2010 (132)
6 OMICIA ss244238870 Aug 29, 2012 (137)
7 OMIM-CURATED-RECORDS ss275516479 Sep 12, 2012 (137)
8 NHLBI-ESP ss342300058 May 09, 2011 (134)
9 ILLUMINA ss479774064 May 04, 2012 (137)
10 ILLUMINA ss482645501 May 04, 2012 (137)
11 1000GENOMES ss490998341 May 04, 2012 (137)
12 EXOME_CHIP ss491436444 May 04, 2012 (137)
13 CLINSEQ_SNP ss491626899 May 04, 2012 (137)
14 ILLUMINA ss781065177 Sep 08, 2015 (146)
15 ILLUMINA ss783573413 Sep 08, 2015 (146)
16 EVA-GONL ss987625991 Aug 21, 2014 (142)
17 1000GENOMES ss1337950281 Aug 21, 2014 (142)
18 EVA_GENOME_DK ss1575200590 Apr 01, 2015 (144)
19 EVA_FINRISK ss1584068499 Apr 01, 2015 (144)
20 EVA_DECODE ss1597297585 Apr 01, 2015 (144)
21 EVA_UK10K_ALSPAC ss1624837850 Apr 01, 2015 (144)
22 EVA_UK10K_TWINSUK ss1667831883 Apr 01, 2015 (144)
23 EVA_EXAC ss1689938867 Apr 01, 2015 (144)
24 EVA_MGP ss1711260114 Apr 01, 2015 (144)
25 ILLUMINA ss1751978697 Sep 08, 2015 (146)
26 ILLUMINA ss1917847932 Feb 12, 2016 (147)
27 WEILL_CORNELL_DGM ss1930991106 Feb 12, 2016 (147)
28 ILLUMINA ss1946285289 Feb 12, 2016 (147)
29 ILLUMINA ss1959271832 Feb 12, 2016 (147)
30 JJLAB ss2026222706 Sep 14, 2016 (149)
31 USC_VALOUEV ss2154496827 Dec 20, 2016 (150)
32 HUMAN_LONGEVITY ss2175798742 Dec 20, 2016 (150)
33 TOPMED ss2338838933 Dec 20, 2016 (150)
34 ILLUMINA ss2632726986 Nov 08, 2017 (151)
35 ILLUMINA ss2632726987 Nov 08, 2017 (151)
36 GNOMAD ss2738305443 Nov 08, 2017 (151)
37 GNOMAD ss2748406782 Nov 08, 2017 (151)
38 GNOMAD ss2890219004 Nov 08, 2017 (151)
39 SWEGEN ss3006689894 Nov 08, 2017 (151)
40 ILLUMINA ss3021250422 Nov 08, 2017 (151)
41 BIOINF_KMB_FNS_UNIBA ss3026902807 Nov 08, 2017 (151)
42 TOPMED ss3123141213 Nov 08, 2017 (151)
43 CSHL ss3349185736 Nov 08, 2017 (151)
44 ILLUMINA ss3634409283 Oct 12, 2018 (152)
45 ILLUMINA ss3640116625 Oct 12, 2018 (152)
46 ILLUMINA ss3641684967 Oct 12, 2018 (152)
47 ILLUMINA ss3644537992 Oct 12, 2018 (152)
48 ILLUMINA ss3651606526 Oct 12, 2018 (152)
49 EGCUT_WGS ss3674105898 Jul 13, 2019 (153)
50 EVA_DECODE ss3690135096 Jul 13, 2019 (153)
51 ACPOP ss3737438745 Jul 13, 2019 (153)
52 ILLUMINA ss3744367882 Jul 13, 2019 (153)
53 ILLUMINA ss3744710142 Jul 13, 2019 (153)
54 EVA ss3748258773 Jul 13, 2019 (153)
55 ILLUMINA ss3772210688 Jul 13, 2019 (153)
56 KHV_HUMAN_GENOMES ss3813633988 Jul 13, 2019 (153)
57 EVA ss3824525802 Apr 26, 2020 (154)
58 EVA ss3825777381 Apr 26, 2020 (154)
59 EVA ss3832193843 Apr 26, 2020 (154)
60 SGDP_PRJ ss3874475414 Apr 26, 2020 (154)
61 FSA-LAB ss3983979617 Apr 26, 2021 (155)
62 EVA ss3986487222 Apr 26, 2021 (155)
63 TOPMED ss4856807391 Apr 26, 2021 (155)
64 1000Genomes NC_000010.10 - 72360387 Oct 12, 2018 (152)
65 The Avon Longitudinal Study of Parents and Children NC_000010.10 - 72360387 Oct 12, 2018 (152)
66 Genetic variation in the Estonian population NC_000010.10 - 72360387 Oct 12, 2018 (152)
67 ExAC NC_000010.10 - 72360387 Oct 12, 2018 (152)
68 FINRISK NC_000010.10 - 72360387 Apr 26, 2020 (154)
69 The Danish reference pan genome NC_000010.10 - 72360387 Apr 26, 2020 (154)
70 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 355887279 (NC_000010.11:70600630:G:A 4162/140294)
Row 355887280 (NC_000010.11:70600630:G:T 1/140300)

- Apr 26, 2021 (155)
71 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 355887279 (NC_000010.11:70600630:G:A 4162/140294)
Row 355887280 (NC_000010.11:70600630:G:T 1/140300)

- Apr 26, 2021 (155)
72 gnomAD - Exomes NC_000010.10 - 72360387 Jul 13, 2019 (153)
73 Genome of the Netherlands Release 5 NC_000010.10 - 72360387 Apr 26, 2020 (154)
74 Medical Genome Project healthy controls from Spanish population NC_000010.10 - 72360387 Apr 26, 2020 (154)
75 Northern Sweden NC_000010.10 - 72360387 Jul 13, 2019 (153)
76 Qatari NC_000010.10 - 72360387 Apr 26, 2020 (154)
77 SGDP_PRJ NC_000010.10 - 72360387 Apr 26, 2020 (154)
78 Siberian NC_000010.10 - 72360387 Apr 26, 2020 (154)
79 TopMed NC_000010.11 - 70600631 Apr 26, 2021 (155)
80 UK 10K study - Twins NC_000010.10 - 72360387 Oct 12, 2018 (152)
81 ALFA NC_000010.11 - 70600631 Apr 26, 2021 (155)
82 ClinVar RCV000014719.5 Apr 26, 2020 (154)
83 ClinVar RCV000224458.1 Oct 12, 2018 (152)
84 ClinVar RCV000456018.2 Oct 12, 2018 (152)
85 ClinVar RCV000547554.4 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
ss207405928, ss482645501, ss491626899, ss1597297585 NC_000010.9:72030392:G:A NC_000010.11:70600630:G:A (self)
50357554, 27952488, 19844146, 162720, 64960, 2214167, 7503226, 12465985, 375874, 10723610, 13033036, 26492394, 7013181, 27952488, ss235229278, ss342300058, ss479774064, ss490998341, ss491436444, ss781065177, ss783573413, ss987625991, ss1337950281, ss1575200590, ss1584068499, ss1624837850, ss1667831883, ss1689938867, ss1711260114, ss1751978697, ss1917847932, ss1930991106, ss1946285289, ss1959271832, ss2026222706, ss2154496827, ss2338838933, ss2632726986, ss2632726987, ss2738305443, ss2748406782, ss2890219004, ss3006689894, ss3021250422, ss3349185736, ss3634409283, ss3640116625, ss3641684967, ss3644537992, ss3651606526, ss3674105898, ss3737438745, ss3744367882, ss3744710142, ss3748258773, ss3772210688, ss3824525802, ss3825777381, ss3832193843, ss3874475414, ss3983979617, ss3986487222 NC_000010.10:72360386:G:A NC_000010.11:70600630:G:A (self)
RCV000014719.5, RCV000224458.1, RCV000456018.2, RCV000547554.4, 45471827, 72353046, 2399056731, ss244238870, ss275516479, ss2175798742, ss3026902807, ss3123141213, ss3690135096, ss3813633988, ss4856807391 NC_000010.11:70600630:G:A NC_000010.11:70600630:G:A (self)
ss52058312 NT_008583.16:20911541:G:A NC_000010.11:70600630:G:A (self)
ss48420743, ss69082996 NT_030059.13:23164850:G:A NC_000010.11:70600630:G:A (self)
2399056731 NC_000010.11:70600630:G:T NC_000010.11:70600630:G:T
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

14 citations for rs35947132
PMID Title Author Year Journal
12229880 Adult onset and atypical presentation of hemophagocytic lymphohistiocytosis in siblings carrying PRF1 mutations. Clementi R et al. 2002 Blood
14739222 Atypical features of familial hemophagocytic lymphohistiocytosis. Busiello R et al. 2004 Blood
14757862 Characterisation of diverse PRF1 mutations leading to decreased natural killer cell activity in North American families with haemophagocytic lymphohistiocytosis. Molleran Lee S et al. 2004 Journal of medical genetics
15342365 A91V is a polymorphism in the perforin gene not causative of an FHLH phenotype. Zur Stadt U et al. 2004 Blood
15728124 A proportion of patients with lymphoma may harbor mutations of the perforin gene. Clementi R et al. 2005 Blood
16720836 Variations of the perforin gene in patients with autoimmunity/lymphoproliferation and defective Fas function. Clementi R et al. 2006 Blood
17311987 Perforin gene mutations in patients with acquired aplastic anemia. Solomou EE et al. 2007 Blood
18661762 Macrophage activation syndrome in 13 children with systemic-onset juvenile idiopathic arthritis. Zeng HS et al. 2008 World journal of pediatrics
22373437 Identification of functional genetic variation in exome sequence analysis. Jaffe A et al. 2011 BMC proceedings
23528102 Association between granzyme B and perforin I polymorphisms and allograft outcomes in Hispanic kidney transplant recipients. Corrales-Tellez E et al. 2013 Clinical transplantation
24033266 A systematic approach to assessing the clinical significance of genetic variants. Duzkale H et al. 2013 Clinical genetics
25741868 Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Richards S et al. 2015 Genetics in medicine
27535533 Analysis of protein-coding genetic variation in 60,706 humans. Lek M et al. 2016 Nature
29304394 Perforin gene variation influences survival in childhood acute lymphoblastic leukemia. Jaworowska A et al. 2018 Leukemia research
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.post676+237644a