rs11830902
Positions:
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001242.5(CD27):c.269-9T>C variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00459 in 1,609,108 control chromosomes in the GnomAD database, including 259 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.023 ( 144 hom., cov: 32)
Exomes 𝑓: 0.0027 ( 115 hom. )
Consequence
CD27
NM_001242.5 splice_polypyrimidine_tract, intron
NM_001242.5 splice_polypyrimidine_tract, intron
Scores
2
Splicing: ADA: 0.0001778
2
Clinical Significance
Conservation
PhyloP100: -0.0250
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.73).
BP6
?
Variant 12-6450164-T-C is Benign according to our data. Variant chr12-6450164-T-C is described in ClinVar as [Benign]. Clinvar id is 473871.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-6450164-T-C is described in Lovd as [Benign].
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0777 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CD27 | NM_001242.5 | c.269-9T>C | splice_polypyrimidine_tract_variant, intron_variant | ENST00000266557.4 | |||
CD27-AS1 | NR_015382.2 | n.1177+177A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD27 | ENST00000266557.4 | c.269-9T>C | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001242.5 | P1 | |||
CD27-AS1 | ENST00000689782.1 | n.100+1305A>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0232 AC: 3526AN: 152108Hom.: 143 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
3526
AN:
152108
Hom.:
Cov.:
32
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: 0.00652 AC: 1613AN: 247298Hom.: 62 AF XY: 0.00485 AC XY: 649AN XY: 133882
GnomAD3 exomes
AF:
AC:
1613
AN:
247298
Hom.:
AF XY:
AC XY:
649
AN XY:
133882
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 AF: 0.00265 AC: 3861AN: 1456882Hom.: 115 Cov.: 32 AF XY: 0.00239 AC XY: 1730AN XY: 724926
GnomAD4 exome
AF:
AC:
3861
AN:
1456882
Hom.:
Cov.:
32
AF XY:
AC XY:
1730
AN XY:
724926
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 ? AF: 0.0232 AC: 3532AN: 152226Hom.: 144 Cov.: 32 AF XY: 0.0224 AC XY: 1667AN XY: 74420
GnomAD4 genome
?
AF:
AC:
3532
AN:
152226
Hom.:
Cov.:
32
AF XY:
AC XY:
1667
AN XY:
74420
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.:
Bravo
AF:
Asia WGS
AF:
AC:
10
AN:
3478
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Lymphoproliferative syndrome 2 Benign:2
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Nov 29, 2023 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
Autoinflammatory syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | Aug 12, 2021 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at