ClinVar Miner

Variants from Giacomini Lab, University of California, San Francisco with conflicting interpretations

Location: United States  Primary collection method: research
Minimum review status of the submission from Giacomini Lab, University of California, San Francisco: Collection method of the submission from Giacomini Lab, University of California, San Francisco:
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
46 50 0 14 17 0 27 54

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.

All submitters
Giacomini Lab, University of California, San Francisco pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 0 4 1 0 0
likely pathogenic 5 0 3 0 0
uncertain significance 15 17 0 4 2
likely benign 0 0 12 0 5

Submitter to submitter summary #

Total submitters: 20
Download table as spreadsheet
Submitter 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
Invitae 0 60 0 9 11 0 21 41
Genome-Nilou Lab 0 21 0 6 4 0 7 17
Baylor Genetics 0 9 0 2 1 0 11 14
Natera, Inc. 0 31 0 4 2 0 5 11
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 4 0 2 0 0 7 9
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories 0 5 0 2 1 0 3 6
Counsyl 0 4 0 2 0 0 4 6
Illumina Laboratory Services, Illumina 0 10 0 0 4 0 1 5
Mendelics 0 0 0 1 0 0 3 4
Fulgent Genetics, Fulgent Genetics 0 8 0 1 1 0 2 4
Revvity Omics, Revvity 0 7 0 0 1 0 2 3
Myriad Genetics, Inc. 0 3 0 1 0 0 1 2
Neuberg Centre For Genomic Medicine, NCGM 0 0 0 1 0 0 1 2
Clinical Molecular Genetics Laboratory, Johns Hopkins All Children's Hospital 0 0 0 0 1 0 0 1
Institute for Genomic Medicine (IGM) Clinical Laboratory, Nationwide Children's Hospital 0 0 0 0 0 0 1 1
Centogene AG - the Rare Disease Company 0 2 0 1 0 0 0 1
HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology 0 0 0 0 0 0 1 1
Genetics and Molecular Pathology, SA Pathology 0 0 0 1 0 0 0 1
Clinical Genomics Program, Stanford Medicine 0 0 0 1 0 0 0 1
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein 0 0 0 0 1 0 0 1

All variants with conflicting interpretations #

Total variants: 54
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_003060.4(SLC22A5):c.1645C>T (p.Pro549Ser) rs11568525 0.02345
NM_003060.4(SLC22A5):c.430C>T (p.Leu144Phe) rs10040427 0.02340
NM_003060.4(SLC22A5):c.1249A>G (p.Met417Val) rs139775414 0.00365
NM_003060.4(SLC22A5):c.59T>A (p.Leu20His) rs144020613 0.00362
NM_003060.4(SLC22A5):c.1463G>A (p.Arg488His) rs28383481 0.00347
NM_003060.4(SLC22A5):c.1590G>T (p.Met530Ile) rs148233131 0.00335
NM_003060.4(SLC22A5):c.1345T>G (p.Tyr449Asp) rs11568514 0.00114
NM_003060.4(SLC22A5):c.934A>G (p.Ile312Val) rs77300588 0.00085
NM_003060.4(SLC22A5):c.34G>A (p.Gly12Ser) rs139203363 0.00066
NM_003060.4(SLC22A5):c.1579G>C (p.Val527Leu) rs145792427 0.00063
NM_003060.4(SLC22A5):c.1441G>A (p.Val481Ile) rs11568513 0.00061
NM_003060.4(SLC22A5):c.1142T>C (p.Met381Thr) rs149730454 0.00056
NM_003060.4(SLC22A5):c.136C>T (p.Pro46Ser) rs202088921 0.00052
NM_003060.4(SLC22A5):c.364G>T (p.Asp122Tyr) rs201082652 0.00043
NM_003060.4(SLC22A5):c.272A>G (p.Asn91Ser) rs546442503 0.00039
NM_003060.4(SLC22A5):c.605T>C (p.Leu202Pro) rs142447950 0.00035
NM_003060.4(SLC22A5):c.287G>C (p.Gly96Ala) rs377767450 0.00029
NM_003060.4(SLC22A5):c.529A>G (p.Met177Val) rs145068530 0.00028
NM_003060.4(SLC22A5):c.1643G>A (p.Arg548Lys) rs150775371 0.00023
NM_003060.4(SLC22A5):c.115T>G (p.Ser39Ala) rs544332057 0.00016
NM_003060.4(SLC22A5):c.904A>G (p.Lys302Glu) rs75783492 0.00016
NM_003060.4(SLC22A5):c.43G>T (p.Gly15Trp) rs267607052 0.00010
NM_003060.4(SLC22A5):c.728A>C (p.Tyr243Ser) rs1321621475 0.00009
NM_003060.4(SLC22A5):c.415G>A (p.Asp139Asn) rs577131769 0.00007
NM_003060.4(SLC22A5):c.1403C>A (p.Thr468Lys) rs386134221 0.00004
NM_003060.4(SLC22A5):c.769C>T (p.Arg257Trp) rs386134203 0.00004
NM_003060.4(SLC22A5):c.1521G>C (p.Leu507Phe) rs778716973 0.00002
NM_003060.4(SLC22A5):c.1409C>T (p.Ser470Phe) rs386134222 0.00001
NM_003060.4(SLC22A5):c.1411C>T (p.Arg471Cys) rs749282641 0.00001
NM_003060.4(SLC22A5):c.1520T>C (p.Leu507Ser) rs1157198543 0.00001
NM_003060.4(SLC22A5):c.1621A>T (p.Met541Leu) rs758158685 0.00001
NM_003060.4(SLC22A5):c.197C>T (p.Thr66Ile) rs1169005119 0.00001
NM_003060.4(SLC22A5):c.338G>A (p.Cys113Tyr) rs727504159 0.00001
NM_003060.4(SLC22A5):c.428C>T (p.Pro143Leu) rs1178584184 0.00001
NM_003060.4(SLC22A5):c.455G>A (p.Gly152Asp) rs747821417 0.00001
NM_003060.4(SLC22A5):c.557T>C (p.Leu186Pro) rs386134197 0.00001
NM_003060.4(SLC22A5):c.629A>G (p.Asn210Ser) rs386134198 0.00001
NM_003060.4(SLC22A5):c.77G>A (p.Ser26Asn) rs772578415 0.00001
NM_003060.4(SLC22A5):c.1064C>T (p.Ser355Leu)
NM_003060.4(SLC22A5):c.1085C>T (p.Ser362Leu) rs886042092
NM_003060.4(SLC22A5):c.1138G>A (p.Ala380Thr)
NM_003060.4(SLC22A5):c.1346A>G (p.Tyr449Cys) rs1183338050
NM_003060.4(SLC22A5):c.248G>T (p.Arg83Leu) rs72552726
NM_003060.4(SLC22A5):c.44G>A (p.Gly15Glu) rs751129547
NM_003060.4(SLC22A5):c.538C>G (p.Gln180Glu) rs1437174685
NM_003060.4(SLC22A5):c.575A>G (p.Asn192Ser)
NM_003060.4(SLC22A5):c.592G>T (p.Val198Leu) rs757979350
NM_003060.4(SLC22A5):c.631T>C (p.Tyr211His) rs780314370
NM_003060.4(SLC22A5):c.641C>T (p.Ala214Val) rs386134199
NM_003060.4(SLC22A5):c.685A>C (p.Ile229Leu)
NM_003060.4(SLC22A5):c.700G>C (p.Gly234Arg)
NM_003060.4(SLC22A5):c.791C>G (p.Thr264Arg) rs201262157
NM_003060.4(SLC22A5):c.797C>T (p.Pro266Leu) rs538372785
NM_003060.4(SLC22A5):c.902C>G (p.Ala301Gly)

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