chr6-31356824-C-CA
Position:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate
The NM_005514.8(HLA-B):c.206_207insT(p.Glu69AspfsTer30) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: 𝑓 0.0062 ( 0 hom., cov: 0)
Exomes 𝑓: 0.0098 ( 495 hom. )
Failed GnomAD Quality Control
Consequence
HLA-B
NM_005514.8 frameshift
NM_005514.8 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -4.91
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
BP6
Variant 6-31356824-C-CA is Benign according to our data. Variant chr6-31356824-C-CA is described in ClinVar as [Benign]. Clinvar id is 2656398.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HLA-B | NM_005514.8 | c.206_207insT | p.Glu69AspfsTer30 | frameshift_variant | 2/8 | ENST00000412585.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HLA-B | ENST00000412585.7 | c.206_207insT | p.Glu69AspfsTer30 | frameshift_variant | 2/8 | NM_005514.8 | P1 | ||
ENST00000603274.1 | n.178_179insA | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 406AN: 65386Hom.: 0 Cov.: 0 FAILED QC
GnomAD3 genomes
AF:
AC:
406
AN:
65386
Hom.:
Cov.:
0
FAILED QC
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.0138 AC: 2255AN: 163622Hom.: 189 AF XY: 0.0154 AC XY: 1350AN XY: 87686
GnomAD3 exomes
AF:
AC:
2255
AN:
163622
Hom.:
AF XY:
AC XY:
1350
AN XY:
87686
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00981 AC: 10438AN: 1064090Hom.: 495 Cov.: 27 AF XY: 0.0107 AC XY: 5634AN XY: 527724
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
10438
AN:
1064090
Hom.:
Cov.:
27
AF XY:
AC XY:
5634
AN XY:
527724
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00620 AC: 406AN: 65452Hom.: 0 Cov.: 0 AF XY: 0.00639 AC XY: 197AN XY: 30820
GnomAD4 genome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
406
AN:
65452
Hom.:
Cov.:
0
AF XY:
AC XY:
197
AN XY:
30820
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | May 01, 2022 | HLA-B: BS1, BS2 - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at