12-6814296-C-T
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_000616.5(CD4):c.369C>T(p.Phe123=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0018 in 1,613,462 control chromosomes in the GnomAD database, including 34 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0096 ( 19 hom., cov: 31)
Exomes 𝑓: 0.00099 ( 15 hom. )
Consequence
CD4
NM_000616.5 synonymous
NM_000616.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0860
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=-0.52).
BP6
Variant 12-6814296-C-T is Benign according to our data. Variant chr12-6814296-C-T is described in ClinVar as [Benign]. Clinvar id is 714504.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=0.086 with no splicing effect.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00956 (1454/152160) while in subpopulation AFR AF= 0.0326 (1353/41472). AF 95% confidence interval is 0.0312. There are 19 homozygotes in gnomad4. There are 663 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 19 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CD4 | NM_000616.5 | c.369C>T | p.Phe123= | synonymous_variant | 4/10 | ENST00000011653.9 | NP_000607.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CD4 | ENST00000011653.9 | c.369C>T | p.Phe123= | synonymous_variant | 4/10 | 1 | NM_000616.5 | ENSP00000011653 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00958 AC: 1456AN: 152042Hom.: 19 Cov.: 31
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GnomAD3 exomes AF: 0.00239 AC: 599AN: 250786Hom.: 4 AF XY: 0.00152 AC XY: 206AN XY: 135572
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GnomAD4 exome AF: 0.000994 AC: 1453AN: 1461302Hom.: 15 Cov.: 32 AF XY: 0.000846 AC XY: 615AN XY: 726916
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GnomAD4 genome AF: 0.00956 AC: 1454AN: 152160Hom.: 19 Cov.: 31 AF XY: 0.00891 AC XY: 663AN XY: 74382
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | May 31, 2018 | - - |
Computational 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