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Annotations, frequency, and bioinformatic prediction scores of variants in select candidate genes Gene KCNMA1 CACNA1H Position [hg19] 10:78846314 16:1252303 Nukleotit change c.1372C>T c.1853C>T Protein change p.Arg458Ter p.Pro618Leu Zygosity Hom Het EXAC frequency - 0.001201 PhyloP score 2.672 4.985 PhyloP prediction Conserved Conserved SIFT score - (0.01) SIFT prediction - Deleterious Polyphen2 score - (0.991) PolyPhen prediction - Probably damaging Mutation taster score 1 0.999 Mutation taster prediction Disease causing Disease causing dbSNP ID - rs60734921 Read depth 170 47 Transkript NM 001161353 NM 021098.2 Exon 11/28 9/35
The RET D898Y mutation was previously reported once in dbSNP (rs587780810) and once in the ClinVar database (RCV000123314.1) as a variant of uncertain significance.
Among these variants, five were identified for the first time in this study (Figure 1), 14 had been reported in the published literature and HGMD (HGMD Professional 2017.2), and nine were previously reported in dbSNP, ExAC, and/or the 1000 Genomes Project database, although phenotypic data were lacking.
dbSNP served as a reference to exclude any known frequent variants.
The NCBI dbSNP, 1000 Genomes, and the in-house database were also involved to filter SNPs .
This variant was also present in dbSNP database with rs764083259 code.
SNP datasets: The polymorphism data for UTY gene investigated in present work was retrieved from NCBI dbSNP (1) database and contained 151 missense, 4 non-sense, 2 splice site at 3' end, 73 UTR at 3' end, 1 splice site at 5' end, 5 UTR at 5' end, 84 coding synonymous, 6 frame shift, 2302 introns and 4 stop gained SNPs.
Los tres SNP genotipificados, estan enumerados en la base de datos de SNP (dbSNP) del Centro Nacional para la Informacion Biotecnologica (NCBI) (32).
SNVs, single nucleotide variants; UTR, untranslated regions; dbSNP, single nucleotide polymorphism database; Indels, small insertions and deletions.
(a) Nucleotide variation and dbSNP reference number.
Single nucleotide polymorphisms (SNPs) with a minor allele frequency (MAF) > 0.1% were classified as benign and were not reported based on the Exome Variant Server (http://evs.gs .washington.edu/EVS), the ExAC browser (http://exac.broadinstitute.org), and dbSNP. Reported variants used nomenclature that is based on the Human Genome Variation Society nomenclature guidelines (http://www.hgvs.org/mutnomen) and internally categorized into five categories (benign, likely benign, variant of uncertain significance, likely pathogenic, and pathogenic); the categories "likely benign," "variant of uncertain significance," and "likely pathogenic" were reported as variants of uncertain significance (VOUSs).
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