Skip to main content

Table 1 Some ClinVar variants with minor reference alleles. Allele frequencies are reported from the Exome Aggregation Consortium (ExAC)

From: Challenges imposed by minor reference alleles on the identification and reporting of clinical variants from exome data

rsID REF ExAC Minor Allele Amino-acid change Conservation ClinVar phenotype or Disease
hg19 hg38 Allele MAF Ref/Alt Rhesus Mouse Amino-acid phenotype risk
rs1169305 A A A 0.004 S/G G N S Maturity onset diabetes pathogenic
rs4784677 C C C 0.006 S/N N N S Bardet-biedl syndrome pathogenic
rs497116 C T T 0.014 R/Q Q Q R Sepsis risk factor
rs6025 T C T 0.02 Q/R R Q Q Factor V Leiden pathogenic
rs283413 A C A 0.02 T/P P P T Parkinson disease risk factor
rs820878 T T T 0.03 L/S S S L Sandhoff disease pathogenic
rs2476601 A A A 0.07 W/R R R W (multiple autoimmune diseases) risk factor
rs450046 C C C 0.08 R/Q Q R Proline Dehydrogenase deficiency pathogenic
rs12021720 T T T 0.09 S/G G G S Maple syrup urine disease pathogenic
rs6003 C C C 0.13 R/H H H R Factor XII deficiency pathogenic
rs1154510 T T T 0.15 T/A A A T Hawkinsinuria pathogenic
rs7076156 A A A 0.21 A/T G A Nephrolithiasis risk factor
rs1801265 G A G 0.23 R/C R R R Dihydropyrimidine dehydrogenase deficiency pathogenic
rs1799983 T T T 0.25 D/E E E D Ischemic heart disease risk factor
rs2227564 T T T 0.25 L/P Q Q L Alzheimer disease risk factor
rs1061170 C C C 0.33 H/Y N W H Basal lamina drusen pathogenic
rs1341667 T T T 0.38 Y/H Y Y H Pre-eclampsia risk factor
rs2073711 A A A 0.43 I/T I I T Lumbar disc disease risk factor
rs237025 G G G 0.44 V/M M V Diabetes mellitus risk factor
rs3733402 G G G 0.46 S/N N N S Prekallikrein deficiency pathogenic
  1. Alleles that changed between assemblies are in bold font