ClinVar Miner

Variants in gene HPS1 with conflicting interpretations

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Y axis minimum submission review status: Y axis collection method:
X axis minimum submission review status: X axis collection method:
Minimum conflict level:
Gene type:
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
971 71 0 27 15 0 2 43

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
pathogenic 0 10 0 0 0
likely pathogenic 10 0 2 0 0
uncertain significance 0 2 0 14 2
likely benign 0 0 14 0 17
benign 0 0 2 17 0

All variants with conflicting interpretations #

Total variants: 43
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_000195.5(HPS1):c.11T>C (p.Val4Ala) rs58548334 0.03653
NM_000195.5(HPS1):c.255+9A>G rs78927693 0.00885
NM_000195.5(HPS1):c.779G>A (p.Arg260Gln) rs56378825 0.00761
NM_000195.5(HPS1):c.1698G>A (p.Ser566=) rs148450315 0.00596
NM_000195.5(HPS1):c.27G>C (p.Glu9Asp) rs7914192 0.00426
NM_000195.5(HPS1):c.*12C>T rs112544050 0.00352
NM_000195.5(HPS1):c.1683C>T (p.Cys561=) rs112337765 0.00297
NM_000195.5(HPS1):c.478C>T (p.Arg160Trp) rs142893758 0.00290
NM_000195.5(HPS1):c.1532+5G>A rs199874645 0.00273
NM_000195.5(HPS1):c.678C>T (p.Ala226=) rs539822608 0.00155
NM_000195.5(HPS1):c.1888G>A (p.Val630Ile) rs139061260 0.00144
NM_000195.5(HPS1):c.669-17T>C rs201014731 0.00143
NM_000195.5(HPS1):c.1406A>G (p.Gln469Arg) rs148978269 0.00133
NM_000195.5(HPS1):c.557C>T (p.Ala186Val) rs1801286 0.00125
NM_000195.5(HPS1):c.198G>A (p.Ser66=) rs115265574 0.00111
NM_000195.5(HPS1):c.787C>T (p.Arg263Trp) rs145042327 0.00065
NM_000195.5(HPS1):c.1438G>A (p.Ala480Thr) rs17109853 0.00054
NM_000195.5(HPS1):c.1928G>A (p.Gly643Glu) rs148225281 0.00042
NM_000195.5(HPS1):c.700C>T (p.Leu234=) rs150444975 0.00039
NM_000195.5(HPS1):c.1533-5G>C rs369658421 0.00016
NM_000195.5(HPS1):c.1846G>A (p.Glu616Lys) rs775570414 0.00012
NM_000195.5(HPS1):c.778C>T (p.Arg260Trp) rs564590745 0.00008
NM_000195.5(HPS1):c.2066G>A (p.Arg689Gln) rs147125175 0.00007
NM_000195.5(HPS1):c.1096C>A (p.Pro366Thr) rs138771756 0.00006
NM_000195.5(HPS1):c.1585A>G (p.Ile529Val) rs569192835 0.00005
NM_000195.5(HPS1):c.2052C>T (p.Ala684=) rs576260502 0.00002
NM_000195.5(HPS1):c.398+2T>C rs1486224265 0.00002
NM_000195.5(HPS1):c.1057C>T (p.Leu353=) rs200850713 0.00001
NM_000195.5(HPS1):c.1744-2A>C rs281865088 0.00001
NM_000195.5(HPS1):c.1858-1G>A rs758797992 0.00001
NM_000195.5(HPS1):c.1940+2T>C rs972096803 0.00001
NM_000195.5(HPS1):c.988-1G>T rs764927038 0.00001
NM_000195.5(HPS1):c.1189del (p.Gln397fs) rs281865084
NM_000195.5(HPS1):c.1397+7_1397+8delinsCT rs886038270
NM_000195.5(HPS1):c.1531C>A (p.Arg511=) rs147748659
NM_000195.5(HPS1):c.1653T>G (p.Thr551=) rs765995574
NM_000195.5(HPS1):c.1657C>T (p.Gln553Ter) rs1591031929
NM_000195.5(HPS1):c.1744-5C>T rs369429846
NM_000195.5(HPS1):c.1925del (p.Gly642fs) rs2136083690
NM_000195.5(HPS1):c.233_242del (p.Asn78fs) rs773323079
NM_000195.5(HPS1):c.678_680delinsTGT (p.Ser227Val) rs1554892764
NM_000195.5(HPS1):c.780dup (p.Arg261fs) rs2136197089
NM_000195.5(HPS1):c.848G>C (p.Gly283Ala) rs74154475

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