chr1-167431874-A-T
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_198053.3(CD247):c.430-128T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0216 in 811,836 control chromosomes in the GnomAD database, including 260 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 ( 32 hom., cov: 33)
Exomes 𝑓: 0.022 ( 228 hom. )
Consequence
CD247
NM_198053.3 intron
NM_198053.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0880
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 -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
Variant 1-167431874-A-T is Benign according to our data. Variant chr1-167431874-A-T is described in ClinVar as [Likely_benign]. Clinvar id is 1203968.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0181 (2759/152310) while in subpopulation NFE AF= 0.0275 (1867/68010). AF 95% confidence interval is 0.0264. There are 32 homozygotes in gnomad4. There are 1322 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 32 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CD247 | NM_198053.3 | c.430-128T>A | intron_variant | ENST00000362089.10 | NP_932170.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CD247 | ENST00000362089.10 | c.430-128T>A | intron_variant | 1 | NM_198053.3 | ENSP00000354782 | A1 |
Frequencies
GnomAD3 genomes AF: 0.0181 AC: 2759AN: 152192Hom.: 32 Cov.: 33
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GnomAD4 exome AF: 0.0223 AC: 14740AN: 659526Hom.: 228 AF XY: 0.0221 AC XY: 7832AN XY: 354970
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GnomAD4 genome AF: 0.0181 AC: 2759AN: 152310Hom.: 32 Cov.: 33 AF XY: 0.0177 AC XY: 1322AN XY: 74482
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 04, 2018 | - - |
Computational scores
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BayesDel_noAF
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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