chr6-31356367-T-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_005514.8(HLA-B):c.419A>C(p.Tyr140Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts 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. Y140D) 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.419A>C | p.Tyr140Ser | missense_variant | 3/8 | ENST00000412585.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HLA-B | ENST00000412585.7 | c.419A>C | p.Tyr140Ser | missense_variant | 3/8 | NM_005514.8 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0190 AC: 685AN: 35964Hom.: 79 Cov.: 3
GnomAD3 exomes AF: 0.215 AC: 40300AN: 187878Hom.: 3187 AF XY: 0.212 AC XY: 21755AN XY: 102434
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.160 AC: 136244AN: 850840Hom.: 16503 Cov.: 17 AF XY: 0.160 AC XY: 68396AN XY: 427478
GnomAD4 genome ? AF: 0.0192 AC: 690AN: 35974Hom.: 82 Cov.: 3 AF XY: 0.0200 AC XY: 340AN XY: 17018
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