ClinVar Miner

Variants with conflicting interpretations between Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia and Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Minimum review status of the submission from Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia: Collection method of the submission from Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia:
Minimum review status of the other submission: Collection method of the other submission:
Minimum conflict level:
ClinVar version:

If a variant has more than two submissions, it may have multiple conflicts and therefore be counted in more than one conflict column. If this is the case, the "Variants with any kind of conflict" cell will be less than the sum of the conflicted variants cells to its left.

Variants with only 1 submission per condition Variants with at least 2 submissions on the same condition and no conflicts Variants with a synonymous conflict
(e.g. benign vs non-pathogenic)
Variants with a confidence conflict
(e.g. benign vs likely benign)
Variants with a benign or likely benign vs uncertain conflict Variants with a category conflict
(e.g. benign vs affects)
Variants with a clinically significant conflict
(e.g. benign vs pathogenic)
Variants with any conflict
153 114 0 25 31 0 7 63

Significance breakdown #

In the table below, cells that correspond to a term paired with itself represent synonymous conflicts, i.e. variants that have been annotated with different terms that map to the same standard term. To compare the terms that were actually submitted, check the box in the filters section at the top of this page.

pathogenic likely pathogenic uncertain significance likely benign benign
likely pathogenic 3 0 1 0 0
uncertain significance 4 2 0 10 18
likely benign 0 0 1 0 13
benign 0 0 2 9 0

All variants with conflicting interpretations #

Total variants: 63
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_013339.4(ALG6):c.391T>C (p.Tyr131His) rs35383149 0.02935
NM_004525.3(LRP2):c.2006G>A (p.Gly669Asp) rs34291900 0.02496
NM_000249.4(MLH1):c.2152C>T (p.His718Tyr) rs2020873 0.02345
NM_000203.5(IDUA):c.1225G>C (p.Gly409Arg) rs11934801 0.01974
NM_194248.3(OTOF):c.2464C>T (p.Arg822Trp) rs80356570 0.01518
NM_000426.4(LAMA2):c.1798G>A (p.Gly600Arg) rs36044314 0.01250
NM_007294.4(BRCA1):c.3119G>A (p.Ser1040Asn) rs4986852 0.01109
NM_000293.3(PHKB):c.555G>T (p.Met185Ile) rs56257827 0.01025
NM_000059.4(BRCA2):c.7319A>G (p.His2440Arg) rs4986860 0.00984
NM_004004.6(GJB2):c.101T>C (p.Met34Thr) rs35887622 0.00966
NM_000059.4(BRCA2):c.3264T>C (p.Pro1088=) rs36060526 0.00793
NM_000059.4(BRCA2):c.7017G>C (p.Lys2339Asn) rs45574331 0.00792
NM_000059.4(BRCA2):c.9730G>A (p.Val3244Ile) rs11571831 0.00792
NM_138694.4(PKHD1):c.7921A>G (p.Thr2641Ala) rs7766366 0.00773
NM_153766.3(KCNJ1):c.1013T>C (p.Met338Thr) rs59172778 0.00742
NM_206933.4(USH2A):c.2522C>A (p.Ser841Tyr) rs111033282 0.00569
NM_152564.5(VPS13B):c.3386A>G (p.Lys1129Arg) rs61759485 0.00451
NM_007194.4(CHEK2):c.470T>C (p.Ile157Thr) rs17879961 0.00434
NM_000383.4(AIRE):c.595G>A (p.Val199Ile) rs74162061 0.00404
NM_000135.4(FANCA):c.4249C>G (p.His1417Asp) rs17227403 0.00362
NM_004004.6(GJB2):c.109G>A (p.Val37Ile) rs72474224 0.00354
NM_000271.5(NPC1):c.2882A>G (p.Asn961Ser) rs34084984 0.00352
NM_006506.5(RASA2):c.17C>T (p.Pro6Leu) rs201352230 0.00349
NM_001384474.1(LOXHD1):c.1570C>T (p.Arg524Cys) rs192376005 0.00295
NM_006231.4(POLE):c.16G>C (p.Gly6Arg) rs202220778 0.00293
NM_004525.3(LRP2):c.92C>T (p.Ala31Val) rs144829356 0.00280
NM_000059.4(BRCA2):c.68-7T>A rs81002830 0.00277
NM_000535.7(PMS2):c.2182A>G (p.Thr728Ala) rs141893001 0.00203
NM_001164508.2(NEB):c.17497G>A (p.Val5833Ile) rs149881695 0.00187
NM_000540.3(RYR1):c.10616G>A (p.Arg3539His) rs143987857 0.00171
NM_000059.4(BRCA2):c.4187A>G (p.Gln1396Arg) rs55969723 0.00168
NM_007294.4(BRCA1):c.2521C>T (p.Arg841Trp) rs1800709 0.00137
NM_003242.6(TGFBR2):c.1119G>A (p.Met373Ile) rs35719192 0.00130
NM_033109.5(PNPT1):c.1525G>A (p.Val509Ile) rs146571352 0.00109
NM_001267550.2(TTN):c.80701A>G (p.Ile26901Val) rs201562505 0.00102
NM_004807.3(HS6ST1):c.1121G>A (p.Ser374Asn) rs61732021 0.00094
NM_005732.4(RAD50):c.3036+5G>A rs181016343 0.00078
NM_001267550.2(TTN):c.87412C>A (p.Pro29138Thr) rs72648227 0.00073
NM_001110556.2(FLNA):c.5251C>T (p.Pro1751Ser) rs56102764 0.00069
NM_002615.7(SERPINF1):c.242C>G (p.Ser81Cys) rs140512665 0.00061
NM_000334.4(SCN4A):c.952T>C (p.Trp318Arg) rs199676994 0.00059
NM_000551.4(VHL):c.241C>T (p.Pro81Ser) rs104893829 0.00039
NM_000051.4(ATM):c.7390T>C (p.Cys2464Arg) rs55801750 0.00038
NM_001110792.2(MECP2):c.*14G>A rs199963992 0.00037
NM_001267550.2(TTN):c.45599C>G (p.Ala15200Gly) rs201057307 0.00033
NM_000051.4(ATM):c.3014A>G (p.Asn1005Ser) rs146531614 0.00028
NM_000535.7(PMS2):c.2324A>G (p.Asn775Ser) rs17420802 0.00025
NM_002878.4(RAD51D):c.196G>A (p.Val66Met) rs56026142 0.00009
NM_000038.6(APC):c.5026A>G (p.Arg1676Gly) rs370560998 0.00006
NM_000038.6(APC):c.7399C>A (p.Pro2467Thr) rs372305287 0.00006
NM_002474.3(MYH11):c.1913C>T (p.Ser638Leu) rs771128441 0.00006
NM_030777.4(SLC2A10):c.313C>T (p.Arg105Cys) rs767864243 0.00005
NM_000527.5(LDLR):c.1061-8T>C
NM_000551.4(VHL):c.257C>G (p.Pro86Arg) rs730882034
NM_000551.4(VHL):c.388G>T (p.Val130Phe) rs104893830
NM_000551.4(VHL):c.407T>C (p.Phe136Ser) rs5030833
NM_000551.4(VHL):c.414A>G (p.Pro138=) rs869025648
NM_001018115.3(FANCD2):c.1278+3_1278+6del rs369823368
NM_001953.4(TYMP):c.929-6_929-3del rs201685922
NM_002693.3(POLG):c.264C>T (p.Phe88=) rs144439703
NM_004004.6(GJB2):c.56G>C (p.Ser19Thr) rs80338941
NM_006767.4(LZTR1):c.651+10_651+46del rs541944601
NM_144997.7(FLCN):c.1177-5_1177-3del rs767671406

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