6-31464003-T-G
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBS1_SupportingBS2
The ENST00000414046.3(HCP5):n.743T>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 0.0287 in 512,480 control chromosomes in the GnomAD database, including 368 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
ENST00000414046.3 non_coding_transcript_exon
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HCP5 | NR_040662.1 | n.733T>G | non_coding_transcript_exon_variant | Exon 2 of 2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HCP5 | ENST00000541196.3 | n.198-50T>G | intron_variant | Intron 2 of 3 | 1 | |||||
HCP5 | ENST00000414046.3 | n.743T>G | non_coding_transcript_exon_variant | Exon 2 of 2 | 4 | |||||
HCP5 | ENST00000670109.1 | n.706T>G | non_coding_transcript_exon_variant | Exon 2 of 2 |
Frequencies
GnomAD3 genomes AF: 0.0247 AC: 3750AN: 151886Hom.: 64 Cov.: 32
GnomAD3 exomes AF: 0.0270 AC: 6123AN: 226874Hom.: 161 AF XY: 0.0292 AC XY: 3603AN XY: 123380
GnomAD4 exome AF: 0.0304 AC: 10943AN: 360476Hom.: 305 Cov.: 0 AF XY: 0.0323 AC XY: 6673AN XY: 206568
GnomAD4 genome AF: 0.0247 AC: 3749AN: 152004Hom.: 63 Cov.: 32 AF XY: 0.0241 AC XY: 1788AN XY: 74312
ClinVar
Submissions by phenotype
Autism spectrum disorder Pathogenic:1
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). -
Abacavir hypersensitivity Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at