chr6-31356423-G-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_005514.8(HLA-B):c.363C>G(p.Ser121Arg) 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. S121N) 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.363C>G | p.Ser121Arg | missense_variant | 3/8 | ENST00000412585.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HLA-B | ENST00000412585.7 | c.363C>G | p.Ser121Arg | missense_variant | 3/8 | NM_005514.8 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.347 AC: 11578AN: 33360Hom.: 4534 Cov.: 3
GnomAD3 exomes AF: 0.710 AC: 125997AN: 177552Hom.: 51124 AF XY: 0.710 AC XY: 68480AN XY: 96486
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.428 AC: 299975AN: 701228Hom.: 113105 Cov.: 14 AF XY: 0.441 AC XY: 154750AN XY: 350816
GnomAD4 genome ? AF: 0.347 AC: 11584AN: 33368Hom.: 4536 Cov.: 3 AF XY: 0.344 AC XY: 5343AN XY: 15510
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