chr6-31356747-GCC-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_005514.8(HLA-B):c.282_283del(p.Gln94HisfsTer4) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.621 in 968,846 control chromosomes in the GnomAD database, including 261,513 homozygotes. Variant has been reported in ClinVar as Benign (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: 𝑓 0.34 ( 5022 hom., cov: 0)
Exomes 𝑓: 0.63 ( 256491 hom. )
Consequence
HLA-B
NM_005514.8 frameshift
NM_005514.8 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -1.06
Genes affected
HLA-B (HGNC:4932): (major histocompatibility complex, class I, B) HLA-B belongs to the HLA class I heavy chain paralogues. This class I molecule is a heterodimer consisting of a heavy chain and a light chain (beta-2 microglobulin). The heavy chain is anchored in the membrane. Class I molecules play a central role in the immune system by presenting peptides derived from the endoplasmic reticulum lumen. They are expressed in nearly all cells. The heavy chain is approximately 45 kDa and its gene contains 8 exons. Exon 1 encodes the leader peptide, exon 2 and 3 encode the alpha1 and alpha2 domains, which both bind the peptide, exon 4 encodes the alpha3 domain, exon 5 encodes the transmembrane region and exons 6 and 7 encode the cytoplasmic tail. Polymorphisms within exon 2 and exon 3 are responsible for the peptide binding specificity of each class one molecule. Typing for these polymorphisms is routinely done for bone marrow and kidney transplantation. Hundreds of HLA-B alleles have been described. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant 6-31356747-GCC-G is Benign according to our data. Variant chr6-31356747-GCC-G is described in ClinVar as [Benign]. Clinvar id is 3060355.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HLA-B | NM_005514.8 | c.282_283del | p.Gln94HisfsTer4 | frameshift_variant | 2/8 | ENST00000412585.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HLA-B | ENST00000412585.7 | c.282_283del | p.Gln94HisfsTer4 | frameshift_variant | 2/8 | NM_005514.8 | P1 | ||
ENST00000603274.1 | n.102_103del | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.341 AC: 15063AN: 44178Hom.: 5020 Cov.: 0
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GnomAD3 exomes AF: 0.729 AC: 147448AN: 202136Hom.: 61708 AF XY: 0.733 AC XY: 80711AN XY: 110080
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GnomAD4 exome AF: 0.634 AC: 586316AN: 924616Hom.: 256491 AF XY: 0.639 AC XY: 293311AN XY: 459196
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
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
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at