Skip to main content
. Author manuscript; available in PMC: 2022 Apr 21.
Published in final edited form as: J Hum Genet. 2021 Oct 8;67(3):137–142. doi: 10.1038/s10038-021-00982-2

Table 1.

Variants presented as pathogenic/likely pathogenic by Chetruengchai and Shotelersuk. ACMG pathogenicity classifications are presented from the original manuscript along with adjusted ACMG criteria and resulting classifications using both Richards et al. and the Bayes combining method.

Gene Genomic Position cDNA Protein # of Individuals ACMG Criteria Presenteda Classification Presented Richards et al. ClinVar Classificationb GnomAD PopMax ACMG Criteriac Post Literature Review Reclassified Richards Reclassified Tavtigian Bayes
BRCA1 chr17:41244913 NM_007300.4:
c.2635G>T		 p.(Glu879*) 1 PVS1, PM2, PP3, PP5 P P P not in gnomAD PVS1, PS4, PM2_Su P P
PALB2 chr16:23641062 NM_024675.4:
c.2411_2412del		 p.(Ser804Cysfs*10) 1 PVS1, PM2, PP5 P P P/LP SAS, maf=0.00011291 PVS1, PS4 P P
PTEN chr10:89720649 NM_000314.8: c.802–2A>G p.(?) 6 PVS1, PM2, PP3, PP5 P P P not in gnomAD PVS1, PS4_Su, PM2_Sue Pe Pe
TGFBR2 chr3:30713619 NM_003242.6:
c.944C>T		 p.(Thr315Met)d 19 PM1, PP2, PP3, PP5, BS2 LP VUS CIP; B(3), LB (5), LP
(1), VUS(2)		 EAS, maf=0.014436 PM1, BS1 VUS LB
DSP chr6:7579930 NM_004415.4:
c.3507C>A		 p.(Tyr1169*) 9 PVS1, PM2, PP3, PP5 P P LP not in gnomAD PVS1, PM2_Sue VUS LPe
PKP2 chr12:32994140 NM_004572.4:
c.1511–1G>C		 p.(?) 1 PVS1, PM2, PP3, PP5 P P P not in gnomAD PVS1, PM2_Su VUS LP
RYR2 chr1:237540658 NM_001035.3:
c.499A>G		 p.(Lys167Glu) 1 PM1, PM2, PP3, PP5 LP LP LP not in gnomAD PM1, PM2_Su, PP3 VUS VUS
TNNT2 chr1:201328372 NM_001276345.2:
c.863G>C		 p.(Arg288Pro) 6 PM2, PM5, PP2, PP3 LP LP CIP; LP(4), P (1), VUS(1) not in gnomAD PS4_M, PM2_Sue, PP3 VUS VUS
TTN chr2:179418821 NM_001256850.1:
c.84094C>T		 p.(Arg28032*) 1 PVS1, PM2, PP3, PP5 P P P/LP not in gnomAD PVS1, PM2_Su VUS LP
TTN chr2:179415988 NM_001256850.1:
c.86348–1G>A		 p.(?) 1 PVS1, PM2, PP3, PP5 P P LP not in gnomAD PVS1_M, PM2_Su VUS VUS
LDLR chr19:11213463 NM_000527.5:
c.313+1G>A		 p.(?) 1 PVS1, PM2, PP3 P P CIP; LB(1), LP (2), P(17) NFE, maf=0.00006156 PVS1_St, PS4, PP1_St, PM2_Su, PS3_M, PP4 P P
LDLR chr19:11215926 NM_000527.5:
c.344G>A		 p.(Arg115His) 1 PM1, PM2, PP2 LP VUS CIP; LB(1), LP(2), P(1), VUS (3) EAS, maf=0.0022597 PS3 VUS VUS
LDLR chr19:11227576 NM_000527.5:
c.1747C>T		 p.(His583Tyr) 3 PM1, PM2, PM5, PP2, PP3 P LP CIP; LB(1), LP(5), P(7), VUS (1) EAS, maf=0.0012029 PS3_Moderate, PS4 (founder), PM3, PP1_M, PP3 P P
LDLR chr19:11221443 NM_000527.5:
c.1056C>A		 p.(Cys352*) 10 PVS1, PM2, PP3, PP5 P P P/LP not in gnomAD PVS1, PS4_Su, PM2_Su P P
MYBPC3 chr11:47367848 NM_000256.3: c.1000G>A p.(Glu334Lys) 16 PM2, PP2, PP3, PP5 LP VUS CIP; B(2), LP(1), P(2), VUS(6) EAS, maf=0.0033385 PS4, PP3, BS1 VUS VUS
MYH7 chr14:23894566 NM_000257.4: c.2348G>A p.(Arg783His) 1 PM1, PM2, PM5, PP2, BP4 LP LP CIP; LP(3), VUS (3) AFR, maf=0.000040054 PM1, PM2_Su, BP4 VUS VUS
KCNQ1 chr11:2608860 NM_000218.3: c.1189C>T p.(Arg397Trp) 1 PM2, PM5, PP2, PP3 LP LP CIP; B(1), LP (3), VUS(9) NFE, maf=0.0003021; AJ, maf=0.00086839 PS4_M, PS3_Su, PP3, BS1 VUS VUS
KCNQ1 chr11:2594172 NM_000218.3: c.877C>T p.(Arg293Cys) 1 PM2, PP2, PP3, PP5 LP VUS CIP; LP(1), VUS (5) SAS, maf=0.0001307 PP3 VUS VUS
SCN5A chr3:38655260 NM_001160161.2: c.677C>T p.(Ala226Val) 1 PM1, PM2, PP2, PP3, PP5 LP LP CIP; B(1), LB(4), LP (1), VUS(5) EAS, maf=0.0013628 PS4, PM1, PP3, BS1 VUS VUS
SCN5A chr3:38603958 NM_001160161.2: c.3749C>T p.(Thr1250Met) 1 PM1, PM2, PP2, PP3, PP5 LP LP CIP; B(1), LP(2), VUS(11) NFE, maf=0.00031312 PM1, PP1, PP3, BS1 VUS VUS
RYR1 chr19: 38951020 NM_000540.3: c.2366G>A p.(Arg789Gln) 1 PM1, PM2, PP2, PP3 LP LP CIP; LB(10), LP (1), VUS(2) AMR, maf=0.0033578 BS1 LB LB
RYR1 chr19: 38931469 NM_000540.3:
c.130C>T		 p.(Arg44Cys) 2 PM2, PP2, PP3, PP5 LP VUS CIP; LP (3), P(1), VUS(8) AMR, maf=0.000029433 PS4_M, PS3_M, PM1, PP3_M LP LP
a

Criteria not applicable are shown in grey.

b

CIP, Conflicting interpretations of pathogenicity; Pathogenic, P; Likely Pathogenic, LP; Variant of Uncertain Significance, VUS; Likely Benign, LB.

c

For modified strength levels: St, Strong; M, moderate; Su, supporting.

d

Alternate nomenclature NM_001024847.2:c.1019C>T; NP_001020018.1:p.Thr340Met.

e

Variant allele frequency higher than expected in the sample set, correct application of PM2/BS1 requires more information regarding cohort.