12-6817197-T-C
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_000616.5(CD4):c.1023T>C(p.Ser341=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.586 in 1,613,520 control chromosomes in the GnomAD database, including 283,795 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.64 ( 32183 hom., cov: 32)
Exomes 𝑓: 0.58 ( 251612 hom. )
Consequence
CD4
NM_000616.5 synonymous
NM_000616.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.232
Genes affected
CD4 (HGNC:1678): (CD4 molecule) This gene encodes the CD4 membrane glycoprotein of T lymphocytes. The CD4 antigen acts as a coreceptor with the T-cell receptor on the T lymphocyte to recognize antigens displayed by an antigen presenting cell in the context of class II MHC molecules. The CD4 antigen is also a primary receptor for entry of the human immunodeficiency virus through interactions with the HIV Env gp120 subunit. This gene is expressed not only in T lymphocytes, but also in B cells, macrophages, granulocytes, as well as in various regions of the brain. The protein functions to initiate or augment the early phase of T-cell activation, and may function as an important mediator of indirect neuronal damage in infectious and immune-mediated diseases of the central nervous system. Multiple alternatively spliced transcript variants encoding different isoforms have been identified in this gene. [provided by RefSeq, May 2020]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BP6
Variant 12-6817197-T-C is Benign according to our data. Variant chr12-6817197-T-C is described in ClinVar as [Benign]. Clinvar id is 1192706.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-6817197-T-C is described in Lovd as [Benign].
BP7
Synonymous conserved (PhyloP=0.232 with no splicing effect.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.897 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CD4 | NM_000616.5 | c.1023T>C | p.Ser341= | synonymous_variant | 7/10 | ENST00000011653.9 | NP_000607.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CD4 | ENST00000011653.9 | c.1023T>C | p.Ser341= | synonymous_variant | 7/10 | 1 | NM_000616.5 | ENSP00000011653 | P1 | |
CD4 | ENST00000437800.6 | n.1261T>C | non_coding_transcript_exon_variant | 5/8 | 2 |
Frequencies
GnomAD3 genomes AF: 0.641 AC: 97451AN: 151924Hom.: 32156 Cov.: 32
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GnomAD3 exomes AF: 0.644 AC: 161626AN: 250894Hom.: 53587 AF XY: 0.640 AC XY: 86712AN XY: 135578
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GnomAD4 exome AF: 0.581 AC: 848783AN: 1461478Hom.: 251612 Cov.: 52 AF XY: 0.584 AC XY: 424404AN XY: 727034
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GnomAD4 genome AF: 0.642 AC: 97542AN: 152042Hom.: 32183 Cov.: 32 AF XY: 0.650 AC XY: 48326AN XY: 74330
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan | Jan 24, 2024 | This variant is classified as Benign based on local population frequency. This variant was detected in 85% of patients studied by a panel of primary immunodeficiencies. Number of patients: 81. Only high quality variants are reported. - |
not provided Benign:1
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Immunodeficiency 79 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 14, 2021 | - - |
Computational scores
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BayesDel_noAF
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CADD
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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