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Table 2 Details of all NGS detected variants across the 10 clinical MPN samples

From: Analysis of genetic variants in myeloproliferative neoplasms using a 22-gene next-generation sequencing panel

Gene

c.DNA

Aa change

Conse-quence

dbSNP

ClinVar assertion/COSMIC ID

Sample

VAF (%)

Sanger

CALR

c.1092_1143del

p.Leu367Thrfs*45

Fs del

NA

Pathogenic/COSM1738055

09, Overt-PMF

10.6

✓

CALR

c.1154_1155insTTGTC

p.Lys385Asnfs*46

Fs ins

rs765476509

COSM1738056

02, ET

15.9

✓

CALR

c.1153_1154insTATGT

p.Lys385Ilefs*46

Fs ins

NA

COSM5985669

01, ET

35.2

✓

CALR

c.1154A > C

p.Lys385Thr

nSNV

rs1024435400

NA

01, ET

35.5

✓

JAK2

c.1849G > T

p.Val617Phe

nSNV

rs77375493

Pathogenic/COSM12600

07, Pre-PMF

12.1

⨉

10, Overt-PMF

12.2

⨉

06, PV

19.2

✓

08, Pre-PMF

53.7

✓

05, PV

66.5

✓

04, PV

72.9

✓

03, ET

88.0

✓

ABL1

c. 1049A > G

p.Asn350Ser

nSNV

rs144448357

NA

07, Pre-PMF

48.8

✓

ASXL1

c.1927_1928insGGGGGGGGTG

GCCCGGGTGGAGGTGGCGG

CGGGGCCACCGATGAGGGG

GGGGGCAGAGGCAGCAGCA

p.Gly646Trpfs*10a

stopgain

rs750318549

NA

04, PV

31.3

✓

ASXL1

c.1772dupA

p.Tyr591*

stopgain

rs762036456

COSM4169775, COSM4169776

10, Overt-PMF

40.8

✓

ASXL1

c.2190del

p.Leu731Tyrfs*12a

Fs del

NA

NA

09, Overt-PMF

38.5

✓

ASXL1

c.4299A > G

p.Gln1433Glna

sSNV

NA

NA

03, ET

49.2

✓

DNMT3A

c.1155G > A

p.Pro385Proc

sSNV

rs368009374

VUS/likely benign

03, ET

51.6

NA

RUNX1

c.924G > T

p.Gln308Hisc

nSNV

rs80314254

Benign

08, Pre-PMF

49.6

✓

SF3B1

c.2098A > G

p.Lys700Glu

nSNV

rs559063155

Likely pathogenic/ COSM84677

08, Pre-PMF

45.6

✓

TET2

c.911C > T

p.Ala304Val

nSNV

NA

COSM5610834, COSM5610835

10, Overt-PMF

50.1

✓

TET2

c.2604T > G

p.Phe868Leu

nSNV

rs147836249

COSM87107

02, ET

48.7

✓

TET2

c.3583A > G

p.Ile1195Val

nSNV

rs568009712

NA

01, ET

49.6

✓

TET2

c.3734A > G

p.Tyr1245Cysa

nSNV

NA

NA

08, Pre-PMF

44.9

✓

TET2

c.3937del

p.Asp1314Metfs*48

Fs del

NA

COSM4383928

08, Pre-PMF

46.3

✓

TET2

c.4893T > A

p.Tyr1631*b

stopgain

NA

COSM97191

02, ET

1.4

NA

TET2

c.4538A > G

p.Glu1513Gly

nSNV

rs553669299

NA

02, ET

51.6

✓

U2AF1

c.470A > C

p.Gln157Pro

nSNV

rs371246226

Likely pathogenic/

06, PV

9.8

⨉

rs371246226

COSM211534, COSM1318797

10, Overt-PMF

42.5

✓

  1. Aa change, amino acid change; Fs del, frameshift deletion; Fs ins, frameshift insertion; ✓, Sanger detected; ⨉, Sanger undetected; NA, data not available
  2. aPutative novel variant
  3. bVariant with low allele frequency, not validated via Sanger sequencing
  4. cVariant of uncertain significance (VUS)/likely benign/benign variant included for validation of the custom NGS panel