GeneBe

ENST00000399492.6:n.485-948_485-947insCCCCCCCCCCCCCCCCCC

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The ENST00000399492.6(CD27-AS1):​n.485-948_485-947insCCCCCCCCCCCCCCCCCC variant causes a intron change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000014 ( 0 hom., cov: 0)

Consequence

CD27-AS1
ENST00000399492.6 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.06

Publications

0 publications found
Variant links:
Genes affected
CD27-AS1 (HGNC:43896): (CD27 antisense RNA 1)
CD27 (HGNC:11922): (CD27 molecule) The protein encoded by this gene is a member of the TNF-receptor superfamily. This receptor is required for generation and long-term maintenance of T cell immunity. It binds to ligand CD70, and plays a key role in regulating B-cell activation and immunoglobulin synthesis. This receptor transduces signals that lead to the activation of NF-kappaB and MAPK8/JNK. Adaptor proteins TRAF2 and TRAF5 have been shown to mediate the signaling process of this receptor. CD27-binding protein (SIVA), a proapoptotic protein, can bind to this receptor and is thought to play an important role in the apoptosis induced by this receptor. [provided by RefSeq, Jul 2008]
CD27 Gene-Disease associations (from GenCC):
  • lymphoproliferative syndrome 2
    Inheritance: AR Classification: STRONG, MODERATE Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)
  • autosomal recessive lymphoproliferative disease
    Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CD27NM_001413266.1 linkc.-315+554_-315+555insGGGGGGGGGGGGGGGGGG intron_variant Intron 1 of 5 NP_001400195.1
CD27NM_001413267.1 linkc.-403+554_-403+555insGGGGGGGGGGGGGGGGGG intron_variant Intron 1 of 6 NP_001400196.1
CD27NM_001413268.1 linkc.-315+66_-315+67insGGGGGGGGGGGGGGGGGG intron_variant Intron 1 of 5 NP_001400197.1
CD27-AS1NR_015382.2 linkn.1517-948_1517-947insCCCCCCCCCCCCCCCCCC intron_variant Intron 4 of 5

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CD27-AS1ENST00000399492.6 linkn.485-948_485-947insCCCCCCCCCCCCCCCCCC intron_variant Intron 5 of 6 1
CD27-AS1ENST00000417058.6 linkn.814-948_814-947insCCCCCCCCCCCCCCCCCC intron_variant Intron 1 of 2 1
CD27-AS1ENST00000537003.2 linkn.1980-948_1980-947insCCCCCCCCCCCCCCCCCC intron_variant Intron 4 of 5 1

Frequencies

GnomAD3 genomes
AF:
0.0000141
AC:
1
AN:
71092
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000257
Gnomad OTH
AF:
0.00
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0000141
AC:
1
AN:
71092
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
32424
show subpopulations
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
0.00
AC:
0
AN:
15452
American (AMR)
AF:
0.00
AC:
0
AN:
6292
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
1930
East Asian (EAS)
AF:
0.00
AC:
0
AN:
1968
South Asian (SAS)
AF:
0.00
AC:
0
AN:
1874
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
3036
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
154
European-Non Finnish (NFE)
AF:
0.0000257
AC:
1
AN:
38872
Other (OTH)
AF:
0.00
AC:
0
AN:
920
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.325
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
-2.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs57782770; hg19: chr12-6553830; API