acca3deffc05c4d8d11590a1cf3d893763254712 angie Thu Oct 31 13:43:05 2019 -0700 dbSnp153: Adding new ucscNotes suggested by Ana Benet: clinvar{Benign,Conflicting,Pathogenic}, rareAll, rareSome. refs #23283 diff --git src/hg/makeDb/trackDb/human/dbSnp153Composite.html src/hg/makeDb/trackDb/human/dbSnp153Composite.html index e34d5b8..d74342c 100644 --- src/hg/makeDb/trackDb/human/dbSnp153Composite.html +++ src/hg/makeDb/trackDb/human/dbSnp153Composite.html @@ -177,30 +177,48 @@ UCSC annotates some properties of interest. These are noted on the item details page, and may be useful to include or exclude affected variants. Some are purely informational:

+ + + + + + + + + + + + + + + + + + @@ -209,30 +227,45 @@ + + + + + + + + + + + +

keyword in data file (dbSnp152.bb)	# in hg19	# in hg38	description
clinvar	454656	453954	Variant is in ClinVar.
clinvarBenign	143844	143696	Variant is in ClinVar with clinical significance of benign and/or likely benign.
clinvarConflicting	7932	7950	Variant is in ClinVar with reports of both benign and pathogenic significance.
clinvarPathogenic	96242	95262	Variant is in ClinVar with clinical significance of pathogenic and/or likely pathogenic.
commonAll	12178426	12430253	Variant is "common", i.e. has a Minor Allele Frequency of at least 1% in all projects reporting frequencies.
commonSome	20534330	20893174	Variant is "common", i.e. has a Minor Allele Frequency of at least 1% in some, but not all, projects reporting frequencies.
diffMajor	Different frequency sources have different major alleles.
overlapDiffClass	106940656	109838613	This variant overlaps another variant with a different type/class.
overlapSameClass	16890303	17228657	This variant overlaps another with the same type/class but different start/end.
rareAll	662571654	681626796	Variant is "rare", i.e. has a Minor Allele Frequency of less than 1% + in all projects reporting frequencies, or has been reported without frequency data.
rareSome	670927558	690089717	Variant is "rare", i.e. has a Minor Allele Frequency of less than 1% + in some, but not all, projects reporting frequencies, or has been reported without + frequency data.
revStrand	3813390	4512600	The orientation of the currently viewed reference genome sequence is different from the orientation of dbSNP's preferred top-level assembly sequence; alleles are presented on the forward strand of the currently viewed reference sequence.

while others may indicate that the reference genome contains a rare variant or sequencing issue:

@@ -340,33 +373,32 @@ ftp://ftp.ncbi.nlm.nih.gov/snp/archive/b153/JSON/, extracted a subset of the information about each variant, and collated it into a bigBed file using the bigDbSnp.as schema with the information necessary for filtering and displaying the variants, as well as a separate file containing more detailed information to be displayed on each variant's details page (dbSnpDetails.as schema).

Data Access

The raw data underlying the UCSC Genome Browser track can be explored interactively with the -Table Browser, -Data Integrator, -or Variant Annotation Integrator. +Table Browser or +Data Integrator. For automated analysis, the track data files can be downloaded from the downloads server for hg38 and hg19 (dbSnp153.bb); the detailed variant properties can be downloaded from hgFixed (dbSnp153Details.tab.gz).

Please refer to our mailing list archives for questions and example queries, or our Data Access FAQ for more information.

keyword in data file (dbSnp152.bb)	# in hg19	# in hg38	description