rs863455
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong
The NM_198053.3(CD247):c.58+29821G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0 ( 0 hom., cov: 32)
Failed GnomAD Quality Control
Consequence
CD247
NM_198053.3 intron
NM_198053.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.39
Publications
11 publications found
Genes affected
CD247 (HGNC:1677): (CD247 molecule) The protein encoded by this gene is T-cell receptor zeta, which together with T-cell receptor alpha/beta and gamma/delta heterodimers, and with CD3-gamma, -delta and -epsilon, forms the T-cell receptor-CD3 complex. The zeta chain plays an important role in coupling antigen recognition to several intracellular signal-transduction pathways. Low expression of the antigen results in impaired immune response. Two alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
CD247 Gene-Disease associations (from GenCC):
- immunodeficiency 25Inheritance: AR Classification: DEFINITIVE, STRONG, LIMITED Submitted by: ClinGen, Ambry Genetics, Labcorp Genetics (formerly Invitae)
- T-B+ severe combined immunodeficiency due to CD3delta/CD3epsilon/CD3zetaInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -4 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_198053.3. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| CD247 | TSL:1 MANE Select | c.58+29821G>T | intron | N/A | ENSP00000354782.5 | P20963-1 | |||
| CD247 | TSL:1 | c.58+29821G>T | intron | N/A | ENSP00000375969.3 | P20963-3 | |||
| CD247 | c.58+29821G>T | intron | N/A | ENSP00000514800.1 | A0A8V8TQY8 |
Frequencies
GnomAD3 genomes 0.00 AC: 0AN: 151908Hom.: 0 Cov.: 32
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome 0.00 AC: 0AN: 151908Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74184
GnomAD4 genome
Data not reliable, filtered out with message: AC0
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151908
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32
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74184
African (AFR)
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41322
American (AMR)
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15262
Ashkenazi Jewish (ASJ)
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3468
East Asian (EAS)
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5174
South Asian (SAS)
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4830
European-Finnish (FIN)
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10550
Middle Eastern (MID)
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314
European-Non Finnish (NFE)
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67988
Other (OTH)
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2090
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ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
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Calibrated prediction
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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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