rs2596574
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000696560.1(HLA-B):c.-858C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0885 in 1,402,738 control chromosomes in the GnomAD database, including 6,566 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
ENST00000696560.1 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DHFRP2 | use as main transcript | n.31366397G>A | intragenic_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HLA-B | ENST00000696560.1 | c.-858C>T | 5_prime_UTR_premature_start_codon_gain_variant | 1/10 | ENSP00000512718.1 | |||||
HLA-B | ENST00000696562.1 | c.-790C>T | 5_prime_UTR_premature_start_codon_gain_variant | 1/9 | ENSP00000512720.1 | |||||
HLA-B | ENST00000696560.1 | c.-858C>T | 5_prime_UTR_variant | 1/10 | ENSP00000512718.1 |
Frequencies
GnomAD3 genomes AF: 0.102 AC: 15563AN: 151900Hom.: 1062 Cov.: 32
GnomAD4 exome AF: 0.0869 AC: 108629AN: 1250720Hom.: 5499 Cov.: 20 AF XY: 0.0861 AC XY: 54435AN XY: 632236
GnomAD4 genome AF: 0.103 AC: 15582AN: 152018Hom.: 1067 Cov.: 32 AF XY: 0.0990 AC XY: 7358AN XY: 74292
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at