rs1052231
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_198053.3(CD247):c.*844A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.826 in 398,660 control chromosomes in the GnomAD database, including 136,198 homozygotes. 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 0.82 ( 51239 hom., cov: 35)
Exomes 𝑓: 0.83 ( 84959 hom. )
Consequence
CD247
NM_198053.3 3_prime_UTR
NM_198053.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.180
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.848 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CD247 | NM_198053.3 | c.*844A>T | 3_prime_UTR_variant | 8/8 | ENST00000362089.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD247 | ENST00000362089.10 | c.*844A>T | 3_prime_UTR_variant | 8/8 | 1 | NM_198053.3 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.819 AC: 124589AN: 152164Hom.: 51196 Cov.: 35
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GnomAD4 exome AF: 0.830 AC: 204472AN: 246378Hom.: 84959 Cov.: 0 AF XY: 0.830 AC XY: 103598AN XY: 124840
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GnomAD4 genome ? AF: 0.819 AC: 124685AN: 152282Hom.: 51239 Cov.: 35 AF XY: 0.821 AC XY: 61127AN XY: 74466
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at