Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_040662(HCP5):n.733T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0247 in 151886 control chromosomes in the gnomAD Genomes database, including 64 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely risk allele,risk factor (no stars).
Verdict is Benign. Variant got -12 ACMG points.
GnomAD3 genomes AF: 0.0247AC: 3750AN: 151886Hom.: 64Cov.: 32 GnomAD3 exomes AF: 0.0270AC: 6123AN: 226874Hom.: 161 AF XY: 0.0292AC XY: 3603AN XY: 123380 GnomAD4 exome AF: 0.0304AC: 10943AN: 360476Hom.: 305 AF XY: 0.0323AC XY: 6673AN XY: 206568
Submissions by phenotype
Drug-induced liver injury due to flucloxacillin
|Pathogenic, no assertion criteria provided||literature only||OMIM||Jul 01, 2009||- -|
Autism spectrum disorder
|Likely risk allele, no assertion criteria provided||clinical testing||Gene Friend Way, National Innovation Center||Jul 28, 2023||A mutation in HLA complex P5. Many recent studies have shown that HCP5 SNP sequences are strongly associated with various chronic and infectious diseases. Several alleles of HLA genes has been reported to be associated with autism, intellectual disability, schizophrenia (PMID: 30976114). rs2395029 is in complete linkage disequilibrium with HLA-B*5701 (PMID: 31421661), which is a risk allele of intellectual disability (PMID: 30976114). -|
|risk factor, no assertion criteria provided||literature only||OMIM||Jul 01, 2009||- -|
Find out SpliceAI and Pangolin per-transcript scores at