chr6-31356754-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_005514.8(HLA-B):c.277G>A(p.Ala93Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A93R) has been classified as Likely benign.
Frequency
Consequence
NM_005514.8 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HLA-B | NM_005514.8 | c.277G>A | p.Ala93Thr | missense_variant | 2/8 | ENST00000412585.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HLA-B | ENST00000412585.7 | c.277G>A | p.Ala93Thr | missense_variant | 2/8 | NM_005514.8 | P1 | ||
ENST00000603274.1 | n.108C>T | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes AF: 0.432 AC: 15957AN: 36896Hom.: 5432 Cov.: 5
GnomAD3 exomes AF: 0.766 AC: 149551AN: 195270Hom.: 64720 AF XY: 0.768 AC XY: 82003AN XY: 106720
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.662 AC: 600088AN: 907044Hom.: 264581 Cov.: 18 AF XY: 0.666 AC XY: 300379AN XY: 450786
GnomAD4 genome AF: 0.433 AC: 15979AN: 36942Hom.: 5437 Cov.: 5 AF XY: 0.426 AC XY: 7462AN XY: 17512
ClinVar
Submissions by phenotype
HLA-B-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 17, 2020 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at