chr1-167431887-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_198053.3(CD247):c.430-141G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0219 in 769,462 control chromosomes in the GnomAD database, including 254 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.018 ( 31 hom., cov: 33)
Exomes 𝑓: 0.023 ( 223 hom. )
Consequence
CD247
NM_198053.3 intron
NM_198053.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.24
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
?
Variant 1-167431887-C-T is Benign according to our data. Variant chr1-167431887-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1217835.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0181 (2756/152328) while in subpopulation NFE AF= 0.0274 (1862/68014). AF 95% confidence interval is 0.0263. There are 31 homozygotes in gnomad4. There are 1320 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 31 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CD247 | NM_198053.3 | c.430-141G>A | intron_variant | ENST00000362089.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD247 | ENST00000362089.10 | c.430-141G>A | intron_variant | 1 | NM_198053.3 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0181 AC: 2756AN: 152210Hom.: 31 Cov.: 33
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GnomAD4 exome AF: 0.0228 AC: 14081AN: 617134Hom.: 223 AF XY: 0.0225 AC XY: 7487AN XY: 333100
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GnomAD4 genome ? AF: 0.0181 AC: 2756AN: 152328Hom.: 31 Cov.: 33 AF XY: 0.0177 AC XY: 1320AN XY: 74504
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 04, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at