Variants identified by long-read sequencing
| Proband ID | Gene(s) affected | HGVS nomenclature | Inheritance | Variant classification | Case-level classification | ACMG/ClinGen evidence codes | SV, SNV or TRE | Step of srGS lossa | Orthogonal validation |
|---|---|---|---|---|---|---|---|---|---|
| 1 | ZBTB20 | NC_000003.12:g.110477273_114639202_inv | De novo | LP | Likely Diagnostic | 2C(+1.00), 5A (+0.15) | SV | Filtering/QC | Yes, Research Sanger of breakpoints |
| 2 | ALS2 | NC_000002.12:g.201720435-201725085_del; NC_000002.12:g.200115181-201739349_del | Biparental | LP; P | Definitive Diagnostic | 2E (+0.90);2D-4 (+0.90), 3B (+0.45) | SVx2 | Filtering/QC | Pending, supported by srGS data |
| 3 | HCFC1 | NC_000023.11:g.153948602_ins4902, NM_005334.3:c.*745_ins4902 | Maternal (X-linked) | VUS | Uncertain | NA | SV | Variant calling | Yes, Research PCR amplification of breakpoints |
| 4 | ABAT, PMM2, USP7, etc. | NC_000016.9:g.(8742452_9220783)dup_ins[(8742452_8879961)_(9000190_9220783)] | De novo | VUS | Uncertain | 2K (+0.30) | SV | Variant calling | Pending |
| 5 | PHOX2B | NM_003924.4:c.741_758dup, p.(Ala255_Ala260dup) | Unknownb | P | Definitive Diagnostic | PS4_M, PM1_Strong, PM2_Moderate, PM6_Moderateb | TRE | Variant calling | Yes, Clinical testinga |
| 6 | AFF3 | NM_001386135.1:c.-64-281_-64-280insGGC[90] | Unknown | VUS | Uncertain | NA | TRE | Variant calling | Pending |
| 7 | SHANK3 | NM_033517.1:c.3161delT, p.(Lys1054Argfs*10) | De novo | P | Definitive Diagnostic | PVS1_VeryStrong, PS2_Strong, PM2_Moderate | SNV | Variant calling | Yes, Clinical Sanger |
| 8 | HNRNPU | NM_031844.3:c.660_661dupAGGCGGCGGA, p.(Gly221ArgfsTer25) | De novo | P | Definitive Diagnostic | PVS1_VeryStrong, PS2_Strong, PM2_Moderate | SNV | Curation (gene-disease association) | Yes, Clinical Sanger |
| 9 | CSNK2B | NM_001320.6:c.202C > T, p.(Gln68Ter) | Paternal | LP | Likely Diagnostic | PVS1_VeryStrong, PM2_Moderate | SNV | Curation (gene-disease association) | Yes, Clinical Sanger |
| 10 | GNB2 | NM_005273.4:c.217G > A, p.(Ala73Thr) | Maternal | LP | Uncertain | PS4_Moderate, PP2_Supporting, PP3_Supporting | SNV | Curation (gene-disease association) | Yes, Clinical Sanger |
| 11 | MCF2 | NM_005369.5:c.2234G > T, p.(Gly745Val) | Maternal (X-linked) | VUS | Uncertain | PM2 | SNV | Curation (gene-disease association) | Yes, Clinical Sanger |
| 12 | NOTCH3 | NM_000435.3c.6409_6410delCT, p.(Leu2137GlyfsTer104) | Paternal | LP | Likely Diagnostic | PVS1_Strong, PM2_Moderate | SNV | Curation (unexpected mechanism) | Yes, Clinical Sanger |
| 13 | AFF4 | NM_014423.4, c.879delA, p.(His294IlefsTer5) | Paternal | VUS | Uncertain | PM2 | SNV | Curation (unexpected mechanism) | Yes, Clinical Sanger |
| 14 | KCNT2, KIF21A | NC_000001.11:g.196329420-196344697_DUP, NM_017641.3:c.847C > T, p.(Arg283Cys); NM_017641.3:c.706C > T, p.(Gln236Ter) | Paternal/biparental | VUS, VUS;LP | Uncertain | 2I (+0.45); PM2, PP3; PVS1, PM2 | SV; SNV(x2) | Curation (unexpected mechanism) | SV Pending, supported by srGS data; SNVs-Clinical Sanger |
| 15 | NRXN1 | NC_000002.12:49922063_49928691del | De novo | VUS | Uncertain | 2E (+0.30), 4C (+0.15), 4M (+0.30) | SV | Curation (unexpected mechanism) | Pending, supported by srGS data |
| 16 | SCN1A | NM_001165963.4:c.4003-603T > C | Paternal | VUS | Uncertain | PM2_Moderate | SNV | Curation (noncoding variation) | Yes, Clinical Sanger |
[i] (SV) Structural variant, (SNV) single nucleotide variant, (TRE) tandem repeat expansion, (P) pathogenic, (LP) likely pathogenic, (VUS) variant of uncertain significance, (NA) not applicable.
[ii] aFiltering/QC, our filtering or prioritization strategy did not accurately present this for curation (or did not at all); Variant calling, the variant was not called or was called incorrectly/inaccurately; Curation, manual curation did not result in flagging of the variant(s).
[iii] bIndependent clinical testing indicated that the PHOX2B expansion was de novo; we only sequenced the proband in our research study.