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Table 3 Likely pathogenic and pathogenic variants considered for clinical actionability in this study

From: The clinical utility and costs of whole-genome sequencing to detect cancer susceptibility variants—a multi-site prospective cohort study

Gene

Classification

Variant (GRCh37)

Index case ID and presenting tumour-associated phenotype(s)

APC

LP

NM_000038.5:c.-38818_-27797del

I102: PS-A

ATM

LP

NM_000051.3:c.1402_1403del

I104: HL, NET-thyroid, URO-PC (metastatic)

NM_000051.3:c.5644C>T

I189: NET-thyroid, URO-RCC

BAP1

LP

NM_004656.3:c.932-151G>A

I099: Brain, BAPoma

BLM

P

NM_000057.3:c.2695C>T

I121: URO-RCC, tunica albuginea cyst in scrotum

BRCA1

P

NM_007294.3:c.68_69del

I142: NET-thyroid, ALL

BRCA2

P

NM_000059.3:c.7805+473_8754+726del

I031: BC, CRC

NM_000059.3:c.3847_3848del

I059: Cholangiocarcinoma

CHEK2

LP

NM_007194.3:c.349A>G

I090: Head and neck, NET-thyroid (papillary)

DICER1

LP

NM_177438.2:c.3300dup

I167: PS-H

P

NM_177438.2:c.2556T>A

I058: OC (Sertoli Leydig); NET-thyroid (follicular)

FANCA

LP

NM_000135.2:c.1007-1G>A

I150: BC, EC

FANCC

P

NM_000136.2:c.67del

I148: Upper GI, URO (mediastinal germ cell tumour)

FANCD2

LP

NM_033084.3:c.783+385_1134+625inv

I114: OC, sarcoma (soft)

FANCI

LP

NM_001113378.1:c.511C>T

I056: OC (benign steroid cell tumour), bilateral benign serous cystadenofibromas, NET (lung carcinoid)

FH

P

NM_000143.3:c.1052C>A

I046: Leiomyosarcomas

LZTR1

LP

NM_006767.3:c.502del

I191: Cervical, melanoma, NET-thyroid, respiratory, history of other benign tumours

MSH6

LP

NM_000179.2:c.1193T>A

I135: Brain

NM_000179.2:c.1723G>T

I126: EC

MUTYH

P

NM_001128425.1:c.1187G>A

I085: Melanoma, myoxi malignant fibrous histiocytoma, CLL

I127: CRC, non-endocrine PC

I156: PS-A

NM_001128425.1:c.536A>G

I148: Upper GI, URO (mediastinal germ cell tumour)

NBN

LP

NM_002485.4:c.156_157del

I176: BC, EC, NET-thyroid

PALB2

LP

NM_024675.3:c.2747_2748+4del

P

NM_024675.3:c.3113G>A

I129: Melanoma, respiratory, sarcoma (soft), RCC

I134: NHL

RAD51D

LP

NM_002878.3:c.748del

I170: URO-seminoma, PC

RET

LP

NM_020975.4:c.2410G>A

I032: BC; respiratory, NET-thyroid (medullary); URO-urogenital carcinoma

SDHA

P

NM_004168.3:c.91C>T

I101: Brain

  1. Somatic translocation identified in index case I079 is not included here. The structural variant caller DELLY was used to determine the breakpoints for complex (structural and copy-number variants)
  2. More detailed presenting tumour-associated phenotype(s) is provided in Additional file 1: Table S1
  3. Abbreviations: ALL acute lymphocytic leukaemia, BC breast cancer, CLL chronic lymphocytic leukaemia, CRC colorectal cancer, EC endometrial cancer, GI gastrointestinal, HL Hodgkin’s Lymphoma, LP likely pathogenic, NET neuroendocrine, NHL Non-Hodgkin’s Lymphoma, OC ovarian cancer, P pathogenic, PC prostate cancer, PS-A polyposis syndrome adenomatous or adenomas, PS-H polyposis syndrome hamartomatous or juvenile polyps, RCC renal cell carcinoma, URO urogenital
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Genome Medicine

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