12-6445137-C-A
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_001242.5(CD27):c.42C>A(p.Thr14Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000687 in 1,455,710 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 6.9e-7 ( 0 hom. )
Consequence
CD27
NM_001242.5 synonymous
NM_001242.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0540
Publications
0 publications found
Genes affected
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]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.34).
BP6
Variant 12-6445137-C-A is Benign according to our data. Variant chr12-6445137-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 1159552.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.054 with no splicing effect.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 6.87e-7 AC: 1AN: 1455710Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 723742 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
1455710
Hom.:
Cov.:
31
AF XY:
AC XY:
1
AN XY:
723742
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33362
American (AMR)
AF:
AC:
0
AN:
43048
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25886
East Asian (EAS)
AF:
AC:
0
AN:
39548
South Asian (SAS)
AF:
AC:
1
AN:
85394
European-Finnish (FIN)
AF:
AC:
0
AN:
53028
Middle Eastern (MID)
AF:
AC:
0
AN:
5644
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1109710
Other (OTH)
AF:
AC:
0
AN:
60090
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Lymphoproliferative syndrome 2 Benign:1
Jul 11, 2019
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
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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