rs41549513
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Benign. The variant received -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_005514.8(HLA-B):c.315G>T(p.Leu105Leu) variant causes a synonymous 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 Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. L105L) has been classified as Likely benign.
Frequency
Genomes: 𝑓 0.0 ( 0 hom., cov: 6)
Exomes 𝑓: 0.0000020 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
HLA-B
NM_005514.8 synonymous
NM_005514.8 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.588
Publications
3 publications found
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 was made for transcript
Our verdict: Benign. The variant received -7 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
Variant 6-31356716-C-A is Benign according to our data. Variant chr6-31356716-C-A is described in ClinVar as Likely_benign. ClinVar VariationId is 2656396.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.588 with no splicing effect.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_005514.8. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| HLA-B | NM_005514.8 | MANE Select | c.315G>T | p.Leu105Leu | synonymous | Exon 2 of 8 | NP_005505.2 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| HLA-B | ENST00000412585.7 | TSL:6 MANE Select | c.315G>T | p.Leu105Leu | synonymous | Exon 2 of 8 | ENSP00000399168.2 | P01889 | |
| HLA-B | ENST00000696559.1 | c.315G>T | p.Leu105Leu | synonymous | Exon 5 of 11 | ENSP00000512717.1 | P01889 | ||
| HLA-B | ENST00000696560.1 | c.315G>T | p.Leu105Leu | synonymous | Exon 4 of 10 | ENSP00000512718.1 | P01889 |
Frequencies
GnomAD3 genomes 0.00 AC: 0AN: 54834Hom.: 0 Cov.: 6
GnomAD3 genomes
AF:
AC:
0
AN:
54834
Hom.:
Cov.:
6
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
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Gnomad ASJ
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Gnomad EAS
AF:
Gnomad SAS
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Gnomad FIN
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Gnomad MID
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Gnomad NFE
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Gnomad OTH
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000196 AC: 2AN: 1021412Hom.: 0 Cov.: 29 AF XY: 0.00000398 AC XY: 2AN XY: 502434 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
2
AN:
1021412
Hom.:
Cov.:
29
AF XY:
AC XY:
2
AN XY:
502434
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
0
AN:
18438
American (AMR)
AF:
AC:
0
AN:
31656
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
12674
East Asian (EAS)
AF:
AC:
0
AN:
22600
South Asian (SAS)
AF:
AC:
0
AN:
48490
European-Finnish (FIN)
AF:
AC:
0
AN:
34772
Middle Eastern (MID)
AF:
AC:
0
AN:
2586
European-Non Finnish (NFE)
AF:
AC:
2
AN:
810496
Other (OTH)
AF:
AC:
0
AN:
39700
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.225
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
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0.60
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0.95
Allele balance
GnomAD4 genome 0.00 AC: 0AN: 54834Hom.: 0 Cov.: 6 AF XY: 0.00 AC XY: 0AN XY: 26284
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
54834
Hom.:
Cov.:
6
AF XY:
AC XY:
0
AN XY:
26284
African (AFR)
AF:
AC:
0
AN:
12492
American (AMR)
AF:
AC:
0
AN:
5022
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
978
East Asian (EAS)
AF:
AC:
0
AN:
1640
South Asian (SAS)
AF:
AC:
0
AN:
922
European-Finnish (FIN)
AF:
AC:
0
AN:
4360
Middle Eastern (MID)
AF:
AC:
0
AN:
68
European-Non Finnish (NFE)
AF:
AC:
0
AN:
28346
Other (OTH)
AF:
AC:
0
AN:
682
Alfa
AF:
Hom.:
ClinVar
ClinVar submissions
View on ClinVar Significance:Likely benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
not provided (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
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
Publications
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