17-40555417-G-T
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_001838.4(CCR7):c.462C>A(p.Arg154Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00333 in 1,613,972 control chromosomes in the GnomAD database, including 132 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.017 ( 68 hom., cov: 32)
Exomes 𝑓: 0.0019 ( 64 hom. )
Consequence
CCR7
NM_001838.4 synonymous
NM_001838.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.39
Genes affected
CCR7 (HGNC:1608): (C-C motif chemokine receptor 7) The protein encoded by this gene is a member of the G protein-coupled receptor family. This receptor was identified as a gene induced by the Epstein-Barr virus (EBV), and is thought to be a mediator of EBV effects on B lymphocytes. This receptor is expressed in various lymphoid tissues and activates B and T lymphocytes. It has been shown to control the migration of memory T cells to inflamed tissues, as well as stimulate dendritic cell maturation. The chemokine (C-C motif) ligand 19 (CCL19/ECL) has been reported to be a specific ligand of this receptor. Signals mediated by this receptor regulate T cell homeostasis in lymph nodes, and may also function in the activation and polarization of T cells, and in chronic inflammation pathogenesis. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Sep 2014]
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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=-0.73).
BP6
Variant 17-40555417-G-T is Benign according to our data. Variant chr17-40555417-G-T is described in ClinVar as [Benign]. Clinvar id is 781364.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=2.39 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0571 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCR7 | ENST00000246657.2 | c.462C>A | p.Arg154Arg | synonymous_variant | 3/3 | 1 | NM_001838.4 | ENSP00000246657.2 | ||
CCR7 | ENST00000579344.1 | c.444C>A | p.Arg148Arg | synonymous_variant | 3/3 | 1 | ENSP00000462631.1 | |||
CCR7 | ENST00000578085.1 | c.273C>A | p.Arg91Arg | synonymous_variant | 2/2 | 3 | ENSP00000463075.1 |
Frequencies
GnomAD3 genomes AF: 0.0173 AC: 2630AN: 152174Hom.: 68 Cov.: 32
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GnomAD3 exomes AF: 0.00457 AC: 1146AN: 250972Hom.: 29 AF XY: 0.00342 AC XY: 464AN XY: 135666
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GnomAD4 exome AF: 0.00187 AC: 2733AN: 1461680Hom.: 64 Cov.: 32 AF XY: 0.00163 AC XY: 1184AN XY: 727142
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GnomAD4 genome AF: 0.0173 AC: 2634AN: 152292Hom.: 68 Cov.: 32 AF XY: 0.0168 AC XY: 1250AN XY: 74482
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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 | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jun 12, 2018 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
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BayesDel_noAF
Benign
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DANN
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at