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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 Aliases 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.

rs78655421

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr7:117530975 (GRCh38.p12) 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>C / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.00163 (205/125568, TOPMED)
A=0.0004 (33/78696, PAGE_STUDY)
A=0.001 (3/4480, Estonian) (+ 3 more)
A=0.003 (10/3854, ALSPAC)
A=0.002 (9/3708, TWINSUK)
A=0.01 (3/600, NorthernSweden)
Clinical Significance
Reported in ClinVar
Gene : Consequence
CFTR : Missense Variant
Publications
20 citations
Genomic View
See rs on genome
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.p12 chr 7 NC_000007.14:g.117530975G>A
GRCh38.p12 chr 7 NC_000007.14:g.117530975G>C
GRCh38.p12 chr 7 NC_000007.14:g.117530975G>T
GRCh37.p13 chr 7 NC_000007.13:g.117171029G>A
GRCh37.p13 chr 7 NC_000007.13:g.117171029G>C
GRCh37.p13 chr 7 NC_000007.13:g.117171029G>T
CFTR RefSeqGene (LRG_663) NG_016465.4:g.70192G>A
CFTR RefSeqGene (LRG_663) NG_016465.4:g.70192G>C
CFTR RefSeqGene (LRG_663) NG_016465.4:g.70192G>T
Gene: CFTR, CF transmembrane conductance regulator (plus strand)
Molecule type Change Amino acid[Codon] SO Term
CFTR transcript NM_000492.3:c.350G>A R [CGC] > H [CAC] Coding Sequence Variant
cystic fibrosis transmembrane conductance regulator NP_000483.3:p.Arg117His R (Arg) > H (His) Missense Variant
CFTR transcript NM_000492.3:c.350G>C R [CGC] > P [CCC] Coding Sequence Variant
cystic fibrosis transmembrane conductance regulator NP_000483.3:p.Arg117Pro R (Arg) > P (Pro) Missense Variant
CFTR transcript NM_000492.3:c.350G>T R [CGC] > L [CTC] Coding Sequence Variant
cystic fibrosis transmembrane conductance regulator NP_000483.3:p.Arg117Leu R (Arg) > L (Leu) 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: 22148 )
ClinVar Accession Disease Names Clinical Significance
RCV000007528.11 Cystic fibrosis Pathogenic
RCV000007529.4 Congenital bilateral absence of the vas deferens Pathogenic
RCV000078997.9 not provided Pathogenic
RCV000190992.1 Cystic fibrosis Pathogenic
RCV000266539.1 Hereditary pancreatitis Pathogenic
RCV000417156.1 ivacaftor response - Efficacy Drug-Response
RCV000763151.1 Bronchiectasis with or without elevated sweat chloride 1,Congenital bilateral absence of the vas deferens,Cystic fibrosis,Hereditary pancreatitis Pathogenic
Allele: C (allele ID: 68432 )
ClinVar Accession Disease Names Clinical Significance
RCV000577567.1 Cystic fibrosis Not-Provided
Allele: T (allele ID: 68433 )
ClinVar Accession Disease Names Clinical Significance
RCV000577295.1 Cystic fibrosis Uncertain-Significance
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 125568 G=0.99833 T=0.00004, A=0.00163
The PAGE Study Global Study-wide 78696 G=0.9996 A=0.0004
The PAGE Study AfricanAmerican Sub 32512 G=0.9995 A=0.0005
The PAGE Study Mexican Sub 10808 G=0.9993 A=0.0007
The PAGE Study Asian Sub 8318 G=1.000 A=0.000
The PAGE Study PuertoRican Sub 7918 G=1.000 A=0.000
The PAGE Study NativeHawaiian Sub 4534 G=1.000 A=0.000
The PAGE Study Cuban Sub 4230 G=1.000 A=0.000
The PAGE Study Dominican Sub 3828 G=1.000 A=0.000
The PAGE Study CentralAmerican Sub 2450 G=1.000 A=0.000
The PAGE Study SouthAmerican Sub 1982 G=0.999 A=0.001
The PAGE Study NativeAmerican Sub 1260 G=1.000 A=0.000
The PAGE Study SouthAsian Sub 856 G=1.00 A=0.00
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.999 A=0.001
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.997 A=0.003
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.998 A=0.002
Northern Sweden ACPOP Study-wide 600 G=0.99 A=0.01
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 C T Note
GRCh38.p12 chr 7 NC_000007.14:...

NC_000007.14:g.117530975=

NC_000007.14:...

NC_000007.14:g.117530975G>A

NC_000007.14:...

NC_000007.14:g.117530975G>C

NC_000007.14:...

NC_000007.14:g.117530975G>T

GRCh37.p13 chr 7 NC_000007.13:...

NC_000007.13:g.117171029=

NC_000007.13:...

NC_000007.13:g.117171029G>A

NC_000007.13:...

NC_000007.13:g.117171029G>C

NC_000007.13:...

NC_000007.13:g.117171029G>T

CFTR RefSeqGene (LRG_663) NG_016465.4:g...

NG_016465.4:g.70192=

NG_016465.4:g...

NG_016465.4:g.70192G>A

NG_016465.4:g...

NG_016465.4:g.70192G>C

NG_016465.4:g...

NG_016465.4:g.70192G>T

CFTR transcript NM_000492.3:c...

NM_000492.3:c.350=

NM_000492.3:c...

NM_000492.3:c.350G>A

NM_000492.3:c...

NM_000492.3:c.350G>C

NM_000492.3:c...

NM_000492.3:c.350G>T

cystic fibrosis transmembrane conductance regulator NP_000483.3:p...

NP_000483.3:p.Arg117=

NP_000483.3:p...

NP_000483.3:p.Arg117His

NP_000483.3:p...

NP_000483.3:p.Arg117Pro

NP_000483.3:p...

NP_000483.3:p.Arg117Leu

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#.

70 SubSNP, 12 Frequency, 9 ClinVar submissions
No Submitter Submission ID Date (Build)
1 ILLUMINA ss161109590 Dec 01, 2009 (131)
2 RSG_JCVI ss262866392 May 09, 2011 (134)
3 OMIM-CURATED-RECORDS ss263193358 Oct 28, 2010 (133)
4 NHLBI-ESP ss342245206 May 09, 2011 (134)
5 ILLUMINA ss482077281 May 04, 2012 (137)
6 ILLUMINA ss483026305 Sep 08, 2015 (146)
7 ILLUMINA ss485814853 May 04, 2012 (137)
8 ILLUMINA ss485827499 May 04, 2012 (137)
9 EXOME_CHIP ss491404778 May 04, 2012 (137)
10 CLINSEQ_SNP ss491913840 May 04, 2012 (137)
11 ILLUMINA ss537652876 Sep 08, 2015 (146)
12 ILLUMINA ss778654287 Sep 08, 2015 (146)
13 ILLUMINA ss780863461 Sep 08, 2015 (146)
14 ILLUMINA ss783353270 Sep 08, 2015 (146)
15 ILLUMINA ss783548025 Sep 08, 2015 (146)
16 ILLUMINA ss784304394 Sep 08, 2015 (146)
17 CLINVAR ss831880564 Nov 05, 2013 (136)
18 CLINVAR ss831880565 Nov 05, 2013 (136)
19 ILLUMINA ss832615340 Sep 08, 2015 (146)
20 ILLUMINA ss834112156 Sep 08, 2015 (146)
21 EVA-GONL ss984713349 Aug 21, 2014 (142)
22 EVA_FINRISK ss1584054660 Apr 01, 2015 (144)
23 EVA_DECODE ss1594298697 Apr 01, 2015 (144)
24 EVA_UK10K_ALSPAC ss1619050184 Apr 01, 2015 (144)
25 EVA_UK10K_TWINSUK ss1662044217 Apr 01, 2015 (144)
26 EVA_EXAC ss1688917392 Apr 01, 2015 (144)
27 EVA_EXAC ss1688917393 Apr 01, 2015 (144)
28 ILLUMINA ss1752660283 Sep 08, 2015 (146)
29 ILLUMINA ss1752660284 Sep 08, 2015 (146)
30 ILLUMINA ss1917821314 Feb 12, 2016 (147)
31 ILLUMINA ss1946218845 Feb 12, 2016 (147)
32 ILLUMINA ss1959045981 Feb 12, 2016 (147)
33 HUMAN_LONGEVITY ss2297204252 Dec 20, 2016 (150)
34 TOPMED ss2466657329 Dec 20, 2016 (150)
35 TOPMED ss2466657330 Dec 20, 2016 (150)
36 ILLUMINA ss2634651964 Nov 08, 2017 (151)
37 GNOMAD ss2736720325 Nov 08, 2017 (151)
38 GNOMAD ss2747910304 Nov 08, 2017 (151)
39 GNOMAD ss2858210673 Nov 08, 2017 (151)
40 AFFY ss2985418225 Nov 08, 2017 (151)
41 AFFY ss2986049743 Nov 08, 2017 (151)
42 SWEGEN ss3001909343 Nov 08, 2017 (151)
43 ILLUMINA ss3022772750 Nov 08, 2017 (151)
44 TOPMED ss3542333408 Nov 08, 2017 (151)
45 TOPMED ss3542333409 Nov 08, 2017 (151)
46 ILLUMINA ss3629898321 Oct 12, 2018 (152)
47 ILLUMINA ss3629898322 Oct 12, 2018 (152)
48 ILLUMINA ss3632556663 Oct 12, 2018 (152)
49 ILLUMINA ss3633475755 Oct 12, 2018 (152)
50 ILLUMINA ss3634201311 Oct 12, 2018 (152)
51 ILLUMINA ss3635138536 Oct 12, 2018 (152)
52 ILLUMINA ss3635138537 Oct 12, 2018 (152)
53 ILLUMINA ss3635880776 Oct 12, 2018 (152)
54 ILLUMINA ss3636872880 Oct 12, 2018 (152)
55 ILLUMINA ss3637633820 Oct 12, 2018 (152)
56 ILLUMINA ss3640845828 Oct 12, 2018 (152)
57 ILLUMINA ss3640845829 Oct 12, 2018 (152)
58 ILLUMINA ss3644951983 Oct 12, 2018 (152)
59 ILLUMINA ss3653307619 Oct 12, 2018 (152)
60 ILLUMINA ss3654179611 Oct 12, 2018 (152)
61 EGCUT_WGS ss3669660952 Jul 13, 2019 (153)
62 EVA_DECODE ss3720540301 Jul 13, 2019 (153)
63 ILLUMINA ss3726475840 Jul 13, 2019 (153)
64 ACPOP ss3735003763 Jul 13, 2019 (153)
65 ILLUMINA ss3744572417 Jul 13, 2019 (153)
66 ILLUMINA ss3745438540 Jul 13, 2019 (153)
67 ILLUMINA ss3745438541 Jul 13, 2019 (153)
68 PAGE_CC ss3771394235 Jul 13, 2019 (153)
69 ILLUMINA ss3772931303 Jul 13, 2019 (153)
70 ILLUMINA ss3772931304 Jul 13, 2019 (153)
71 The Avon Longitudinal Study of Parents and Children NC_000007.13 - 117171029 Oct 12, 2018 (152)
72 Genetic variation in the Estonian population NC_000007.13 - 117171029 Oct 12, 2018 (152)
73 ExAC

Submission ignored due to conflicting rows:
Row 8997386 (NC_000007.13:117171028:G:G 120175/120360, NC_000007.13:117171028:G:A 185/120360)
Row 8997387 (NC_000007.13:117171028:G:G 120359/120360, NC_000007.13:117171028:G:T 1/120360)

- Oct 12, 2018 (152)
74 ExAC

Submission ignored due to conflicting rows:
Row 8997386 (NC_000007.13:117171028:G:G 120175/120360, NC_000007.13:117171028:G:A 185/120360)
Row 8997387 (NC_000007.13:117171028:G:G 120359/120360, NC_000007.13:117171028:G:T 1/120360)

- Oct 12, 2018 (152)
75 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 106211043 (NC_000007.13:117171028:G:G 31359/31392, NC_000007.13:117171028:G:A 33/31392)
Row 106211044 (NC_000007.13:117171028:G:G 31391/31392, NC_000007.13:117171028:G:T 1/31392)

- Jul 13, 2019 (153)
76 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 106211043 (NC_000007.13:117171028:G:G 31359/31392, NC_000007.13:117171028:G:A 33/31392)
Row 106211044 (NC_000007.13:117171028:G:G 31391/31392, NC_000007.13:117171028:G:T 1/31392)

- Jul 13, 2019 (153)
77 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 5883426 (NC_000007.13:117171028:G:G 250581/250954, NC_000007.13:117171028:G:A 373/250954)
Row 5883427 (NC_000007.13:117171028:G:G 250951/250954, NC_000007.13:117171028:G:T 3/250954)

- Jul 13, 2019 (153)
78 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 5883426 (NC_000007.13:117171028:G:G 250581/250954, NC_000007.13:117171028:G:A 373/250954)
Row 5883427 (NC_000007.13:117171028:G:G 250951/250954, NC_000007.13:117171028:G:T 3/250954)

- Jul 13, 2019 (153)
79 Northern Sweden NC_000007.13 - 117171029 Jul 13, 2019 (153)
80 The PAGE Study NC_000007.14 - 117530975 Jul 13, 2019 (153)
81 TopMed NC_000007.14 - 117530975 Oct 12, 2018 (152)
82 UK 10K study - Twins NC_000007.13 - 117171029 Oct 12, 2018 (152)
83 ClinVar RCV000007528.11 Jul 13, 2019 (153)
84 ClinVar RCV000007529.4 Oct 12, 2018 (152)
85 ClinVar RCV000078997.9 Jul 13, 2019 (153)
86 ClinVar RCV000190992.1 Oct 12, 2018 (152)
87 ClinVar RCV000266539.1 Oct 12, 2018 (152)
88 ClinVar RCV000417156.1 Oct 12, 2018 (152)
89 ClinVar RCV000577295.1 Oct 12, 2018 (152)
90 ClinVar RCV000577567.1 Oct 12, 2018 (152)
91 ClinVar RCV000763151.1 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
ss485827499, ss491913840, ss1594298697 NC_000007.12:116958264:G:A NC_000007.14:117530974:G:A (self)
21617721, 15399200, 8288628, 21617721, ss342245206, ss482077281, ss483026305, ss485814853, ss491404778, ss537652876, ss778654287, ss780863461, ss783353270, ss783548025, ss784304394, ss832615340, ss834112156, ss984713349, ss1584054660, ss1619050184, ss1662044217, ss1688917392, ss1752660283, ss1752660284, ss1917821314, ss1946218845, ss1959045981, ss2466657329, ss2634651964, ss2736720325, ss2747910304, ss2858210673, ss2985418225, ss2986049743, ss3001909343, ss3022772750, ss3629898321, ss3629898322, ss3632556663, ss3633475755, ss3634201311, ss3635138536, ss3635138537, ss3635880776, ss3636872880, ss3637633820, ss3640845828, ss3640845829, ss3644951983, ss3653307619, ss3654179611, ss3669660952, ss3735003763, ss3744572417, ss3745438540, ss3745438541, ss3772931303, ss3772931304 NC_000007.13:117171028:G:A NC_000007.14:117530974:G:A (self)
RCV000007528.11, RCV000007529.4, RCV000078997.9, RCV000190992.1, RCV000266539.1, RCV000417156.1, RCV000763151.1, 615704, 374154501, ss263193358, ss2297204252, ss3542333408, ss3720540301, ss3726475840, ss3771394235 NC_000007.14:117530974:G:A NC_000007.14:117530974:G:A (self)
ss161109590, ss262866392 NT_007933.15:55203871:G:A NC_000007.14:117530974:G:A (self)
RCV000577567.1, ss831880564 NC_000007.14:117530974:G:C NC_000007.14:117530974:G:C (self)
ss1688917393, ss2466657330, ss2736720325, ss2747910304, ss2858210673 NC_000007.13:117171028:G:T NC_000007.14:117530974:G:T (self)
RCV000577295.1, 374154501, ss831880565, ss3542333409 NC_000007.14:117530974:G:T NC_000007.14:117530974: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.

20 citations for rs78655421
PMID Title Author Year Journal
1937486 Hereditary disorders in Saguenay-Lac-St-Jean (Quebec, Canada). De Braekeleer M et al. 1991 Human heredity
2349952 Complex alleles of the acid beta-glucosidase gene in Gaucher disease. Latham T et al. 1990 American journal of human genetics
7506096 A mutation in CFTR produces different phenotypes depending on chromosomal background. Kiesewetter S et al. 1993 Nature genetics
7692051 Male infertility as the only presenting sign of cystic fibrosis when homozygous for the mild mutation R117H. Bienvenu T et al. 1993 Journal of medical genetics
8421472 High frequency of the R117H cystic fibrosis mutation in patients with congenital absence of the vas deferens. Gervais R et al. 1993 The New England journal of medicine
11180668 European Epidemiologic Registry of Cystic Fibrosis (ERCF): comparison of major disease manifestations between patients with different classes of mutations. Koch C et al. 2001 Pediatric pulmonology
11280952 Laboratory standards and guidelines for population-based cystic fibrosis carrier screening. Grody WW et al. 2001 Genetics in medicine
11746017 Cystic fibrosis: a further case of an asymptomatic compound heterozygote. White SM et al. 2001 American journal of medical genetics
18456578 Consensus on the use and interpretation of cystic fibrosis mutation analysis in clinical practice. Castellani C et al. 2008 Journal of cystic fibrosis
19774621 Clinical and molecular characterization of S1118F-CFTR. Penmatsa H et al. 2009 Pediatric pulmonology
19880712 The very low penetrance of cystic fibrosis for the R117H mutation: a reappraisal for genetic counselling and newborn screening. Thauvin-Robinet C et al. 2009 Journal of medical genetics
22992668 Pharmacogenomics knowledge for personalized medicine. Whirl-Carrillo M et al. 2012 Clinical pharmacology and therapeutics
23757202 Free the data: one laboratory's approach to knowledge-based genomic variant classification and preparation for EMR integration of genomic data. Bean LJ et al. 2013 Human mutation
23820649 Where genotype is not predictive of phenotype: towards an understanding of the molecular basis of reduced penetrance in human inherited disease. Cooper DN et al. 2013 Human genetics
23974870 Defining the disease liability of variants in the cystic fibrosis transmembrane conductance regulator gene. Sosnay PR et al. 2013 Nature genetics
25514096 PharmGKB summary: very important pharmacogene information for CFTR. McDonagh EM et al. 2015 Pharmacogenetics and genomics
25698453 Ivacaftor as salvage therapy in a patient with cystic fibrosis genotype F508del/R117H/IVS8-5T. Carter S et al. 2015 Journal of cystic fibrosis
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
26070913 Efficacy and safety of ivacaftor in patients with cystic fibrosis who have an Arg117His-CFTR mutation: a double-blind, randomised controlled trial. Moss RB et al. 2015 The Lancet. Respiratory medicine
26324139 The Role of Ivacaftor in Severe Cystic Fibrosis in a Patient With the R117H Mutation. Ronan NJ et al. 2015 Chest

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.post288+114f6e8