Geisinger Medical Laboratories/Geisinger Proven Diagnostics Test Catalog

Order Display Name: Geisinger Epic Procedure Code Or ID CPT Code:  

MYGENVAR CYSTIC FIBROSIS-CFTR GENE (139 VARIANTS), CARRIER SCREENING, NEXT GENERATION SEQUENCING

ORDERING INFORMATION:
Geisinger Epic Procedure Code: LAB6018         Geisinger Epic ID: 183532

SPECIMEN COLLECTION
Specimen type:
 Whole blood
Preferred collection container:
Alternate Collection Container:
6 mL pink-top K2 EDTA tube
Specimen required:
3 mL lavendar EDTA whole blood; minimum 0.5 mL.
Special notes:
 NO SHARED SPECIMENS WITH OTHER LABORATORY DEPARTMENTS. May be combined with other Molecular Diagnostic tests. For genetic testing, original tube required. Isolated/extracted nucleic acids are acceptable only from CLIA-certified laboratories or a laboratory meeting equivalent requirements as determined by CAP and/or CMS.
SPECIMEN PROCESSING
Specimen processing instructions:
Mix well. Do not centrifuge. 
Transport temperature:
 Refrigerated: 2-8°C
Specimen stability:
 Refrigerated (2-8°C): 4 weeks
Rejection criteria:
 Specimen collected in heparin (green-top) tube will be rejected. Frozen whole blood specimens will be rejected. Stability limits exceeded. Shared or comingled specimens.
TEST DETAILS
Reference interval:
 Negative. No variant is detected in the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) gene carrier screen test.
CPT code(s):
 81220
Note: The billing party has sole responsibility for CPT coding.  Any questions regarding coding should be directed to the payer being billed.  The CPT codes provided by GML are based on AMA guidelines and are for informational purposes only.
Test includes:
 This test detects 139 Cystic fibrosis (CF)-causing variants:
Variant (Display Name) Nucleotide Change (DNA Change) Amino Acid Change Legacy Name
M1V NM_000492.4: c.1A>G p.Met1Val  
  NM_000492.4:c.54-5940_ 273+10250del p.? CFTR dele2,3
Q39* NM_000492.4:c.115C>T p.Gln39Ter  
E60* NM_000492.4:c.178G>T p.Glu60Ter  
P67L NM_000492.4:c.200C>T p.Pro67Leu  
R75* NM_000492.4:c.223C>T p.Arg75Ter  
G85E NM_000492.4:c.254G>A p.Gly85Glu  
L88Ifs*22 NM_000492.4:c.262_263delTT p.Leu88IlefsTer22 394delTT
  NM_000492.4:c.273+1G>A p.? 405+1G>A (c.273+1G>A)
  NM_000492.4:c.274-1G>A p.? 406-1G>A
E92K NM_000492.4:c.274G>A p.Glu92Lys  
E92* NM_000492.4:c.274G>T p.Glu92Ter  
Q98* NM_000492.4:c.292C>T p.Gln98Ter  
Y109Gfs*4 NM_000492.4:c.325_327delTATinsG p.Tyr109GlyfsTer4 457TAT>G
D110H NM_000492.4:c.328G>C p.Asp110His  
R117C NM_000492.4:c.349C>T p.Arg117Cys  
R117H NM_000492.4:c.350G>A p.Arg117His  
Y122* NM_000492.4:c.366T>A p.Tyr122Ter  
I148Lfs*5 NM_000492.4:c.442delA p.Ile148LeufsTer5 574delA
  NM_000492.4:c.489+1G>T p.? 621+1G>T
I177Mfs*12 NM_000492.4:c.531delT p.Ile177MetfsTer12 663delT
G178R NM_000492.4:c.532G>A p.Gly178Arg  
  NM_000492.4:c.579+1G>T p.? 711+1G>T
  NM_000492.4:c.579+3A>G p.? 711+3A>G
  NM_000492.4:c.579+5G>A p.? 711+5G>A
  NM_000492.4:c.580-1G>T p.? 712-1G>T
H199Y NM_000492.4:c.595C>T p.His199Tyr  
P205S NM_000492.4:c.613C>T p.Pro205Ser  
L206W NM_000492.4:c.617T>G p.Leu206Trp  
Q220* NM_000492.4:c.658C>T p.Gln220*  
G241Efs*13 NM_000492.4:c.720_ 741delAGGGAGAAT GATGATGAAGTAC p.Gly241GlufsTer13 852del22
F316Lfs*12 NM_000492.4:c.948delT p.Phe316LeufsTer12 1078delT
G330* NM_000492.4:c.988G>T p.Gly330*  
R334W NM_000492.4:c.1000C>T p.Arg334Trp  
I336K NM_000492.4:c.1007T>A p.Ile336Lys  
T338I NM_000492.4:c.1013C>T p.Thr338Ile  
S341P NM_000492.4:c.1021T>C p.Ser341Pro  
F342Hfs*28 NM_000492.4:c.1022_ 1023insTC p.Phe342HisfsTer28 1154insTC
R347H NM_000492.4:c.1040G>A p.Arg347His  
R347P NM_000492.4:c.1040G>C p.Arg347Pro  
R352Q NM_000492.4:c.1055G>A p.Arg352Gln  
W361Gfs*8 NM_000492.4:c.1081delT p.Trp361GlyfsTer8 1213delT
  NM_000492.4:c.1116+1G>A p.? 1248+1G>A
Q378Afs*4 NM_000492.4:c.1127_1128insA p.Gln378AlafsTer4 1259insA
W401* NM_000492.4:c.1202G>A p.Trp401Ter  
W401* NM_000492.4:c.1203G>A p.Trp401Ter  
  NM_000492.4:c.1209+1G>A p.? 1341+1G>A
I444Rfs*3 NM_000492.4:c.1329_ 1330insAGAT p.Ile444ArgfsTer3 1461ins4
A455E NM_000492.4:c..1364C>A p.Ala455Glu  
  NM_000492.4:c.1393-1G>A p.? 1525-1G>A
S466*  NM_000492.4:c.1397C>A p.Ser466Ter  
S466* NM_000492.4:c.1397C>G p.Ser466Ter  
L467P NM_000492.4:c.1400T>C p.Leu467Pro  
G473Efs*54 NM_000492.4:c.1418delG p.Gly473GlufsTer54 1548delG 
S489* NM_000492.4:c.1466C>A p.Ser489Ter  
S492F NM_000492.4:c.1475C>T p.Ser492Phe  
Q493* NM_000492.4:c.1477C>T p.Gln493Ter  
I506V NM_000492.4:c.1516A>G p.Ile506Val  
I507V NM_000492.4:c.1519A>G p.Ile507Val  
I507del NM_000492.4:c.1519_1521delATC p.Ile507del  
F508del NM_000492.4:c.1521_ 1523delCTT p.Phe508del  
F508C NM_000492.4:c.1523T>G p.Phe508Cys  
Y515* NM_000492.4:c.1545_ 1546delTA p.Tyr515Ter 1677delTA
V520F NM_000492.4:c.1558G>T p.Val520Phe  
Q525* NM_000492.4:c.1573C>T p.Gln525Ter  
  NM_000492.4:c.1585-8G>A p.? 1717-8G>A
  NM_000492.4:c.1585-1G>A p.? 1717-1G>A
G542* NM_000492.4:c.1624G>T p.Gly542Ter  
S549R NM_000492.4:c.1645A>C p.Ser549Arg  
S549N NM_000492.4:c.1646G>A p.Ser549Asn  
S549R NM_000492.4:c.1647T>G p.Ser549Arg  
G551D NM_000492.4:c.1652G>A p.Gly551Asp  
Q552* NM_000492.4:c.1654C>T p.Gln552Ter  
R553* NM_000492.4:c.1657C>T p.Arg553Ter  
A559T NM_000492.4:c.1675G>A p.Ala559Thr  
R560T NM_000492.4:c.1679G>C p.Arg560Thr  
R560K NM_000492.4:c.1679G>A p.Arg560Lys  
  NM_000492.4:c.1679+1.6kbA>G p.? 1811+1.6kbA>G
  NM_000492.4:c.1680-1G>A p.? 1812-1G>A
E585* NM_000492.4:c.1753G>T p.Glu585Ter  
  NM_000492.4:c.1766+1G>A p.? 1898+1G>A (c.1766+1G>A)
  NM_000492.4:c.1766+3A>G p.? 1898+3A>G
L671* NM_000492.4:c.2012delT p.Leu671Ter 2143delT
K684Sfs*38 NM_000492.4:c.2051_ 2052delAAinsG p.Lys684SerfsTer38 2183AA >G
Q685Tfs*4 NM_000492.4:c.2052_2053insA p.Gln685ThrfsTer4 2184insA
K684Nfs*38 NM_000492.4:c.2052delA p.Lys684AsnfsTer38 2184delA
R709* NM_000492.4:c.2125C>T p.Arg709Ter  
K710* NM_000492.4:c.2128A>T p.Lys710Ter  
E726Rfs*4 NM_000492.4:c.2175_2176insA p.Glu726ArgfsTer4 2307insA
L732* NM_000492.4:c.2195T>G p.Leu732Ter  
V739Yfs*16 NM_000492.4:c.2215delG p.Val739TyrfsTer16 2347delG
R764* NM_000492.4:c.2290C>T p.Arg764Ter  
L818Wfs*3 NM_000492.4:c.2453delT p.Leu818TrpfsTer3 2585delT
E822* NM_000492.4:c.2464G>T p.Glu822Ter  
  NM_000492.4:c.2490+1G>A p.? 2622+1G>A
E831* NM_000492.4:c.2491G>T p.Glu831Ter  
W846* NM_000492.4:c.2537G>A p.Trp846Ter  
R851* NM_000492.4:c.2551C>T p.Arg851Ter  
F861Lfs*3 NM_000492.4:c.2583delT p.Phe861LeufsTer3 2711delT
  NM_000492.4:c.2657+5G>A p.? 2789+5G>A
Q890* NM_000492.4:c.2668C>T p.Gln890Ter  
L927P NM_000492.4:c.2780T>C p.Leu927Pro  
S945L NM_000492.4:c.2834C>T p.Ser945Leu  
A959Hfs*9 NM_000492.4:c.2875delG p.Ala959HisfsTer9 3007delG
G970R NM_000492.4:c.2908G>C p.Gly970Arg  
  NM_000492.4:c.2988+1G>A p.? 3120+1G>A
  NM_000492.4:c.2988G>A p.Gln996= 3120G>A
  NM_000492.4:c.2989-1G>A p.? 3121-1G>A
  NM_000492.4:c.3140-26A>G p.? 3272-26A>G
L1065P NM_000492.4:c.3194T>C p.Leu1065Pro  
R1066C NM_000492.4:c.3196C>T p.Arg1066Cys  
R1066H NM_000492.4:c.3197G>A p.Arg1066His  
L1077P NM_000492.4:c.3230T>C p.Leu1077Pro  
W1089* NM_000492.4:c.3266G>A p.Trp1089Ter  
Y1092* NM_000492.4:c.3276C>A p.Tyr1092Ter  
Y1092* NM_000492.4:c.3276C>G p.Tyr1092Ter  
M1101K NM_000492.4:c.3302T>A p.Met1101Lys  
E1104* NM_000492.4:c.3310G>T p.Glu1104Ter  
R1158* NM_000492.4:c.3472C>T p.Arg1158Ter  
R1162* NM_000492.4:c.3484C>T p.Arg1162Ter  
K1177fs*15 NM_000492.4:c.3528delC p.Lys1177SerfsTer15 3659delC
S1196* NM_000492.4:c.3587C>G p.Ser1196Ter  
W1204* NM_000492.4:c.3611G>A p.Trp1204Ter  
W1204* NM_000492.4:c.3612G>A p.Trp1204Ter  
T1220Kfs*8 NM_000492.4:c.3659delC p.Thr1220LysfsTer8 3791delC
  NM_000492.4:c.3717+12191C>T p.? 3849+10kbC>T
G1244E NM_000492.4:c.3731G>A p.Gly1244Glu  
K1250Rfs*9 NM_000492.4:c.3744delA p.Lys1250ArgfsTer9 3876delA
S1251N NM_000492.4:c.3752G>A p.Ser1251Asn  
L1258Ffs*7 NM_000492.4:c.3773_3774insT p.Leu1258PhefsTer7 3905insT
W1282* NM_000492.4:c.3846G>A p.Trp1282Ter  
  NM_000492.4:c.3873+1G>A p.? 4005+1G>A
S1297Ffs*5 NM_000492.4:c.3884_3885insT p.Ser1297PhefsTer5 4016insT
N1303K NM_000492.4:c.3909C>G p.Asn1303Lys  
Q1313* NM_000492.4:c.3937C>T p.Gln1313Ter  
  NM_000492.4:c.3964-78_ 4242+577del p.? CFTRdele22,23
V1360Tfs*3 NM_000492.4:c.4077_ 4080delTGTTinsAA p.Val1360ThrfsTer3 4209TGTT>AA
E1418Rfs*14 NM_000492.4:c.4251delA p.Glu1418ArgfsTer14 4382delA
  NM_000492.4:c.1210-12T[5_9]   5T/7T/9T PolyT
  NM_000492.4:c.1210-34TG[9_13]   PolyTG
Methodology:
Polymerase Chain Reaction (PCR)
Next Generation Sequencing
Synonyms:
CF PCR, cystic fibrosis, cystic fibrosis PCR, cystic fibrosis mutation, CF mutation, CF genotype, cystic fibrosis genotype, CF DNA, cystic fibrosis DNA, CFTR, cystic fibrosis transmembrane conductance.
Clinical significance:
This test is used for cystic fibrosis (CF) carrier screening in adults of reproductive age, in confirmatory diagnostic testing of newborns and children, and as an initial test to aid in the diagnosis of individuals with suspected CF.
Doctoral Director(s:)
Yi Ding MD, PhD    
Review Date: 03/22/2023

Performing Locations

Geisinger Medical Center

Performing laboratory: Molecular Diagnostics
Technical Lead: Ronnie Rovenolt, Becky Knock
Frequency: Biweekly
Performed STAT? No
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