1-161506437-C-T
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Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_001136219.3(FCGR2A):c.210C>T(p.Ser70Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00249 in 1,614,198 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0020 ( 1 hom., cov: 32)
Exomes 𝑓: 0.0025 ( 2 hom. )
Consequence
FCGR2A
NM_001136219.3 synonymous
NM_001136219.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.476
Genes affected
FCGR2A (HGNC:3616): (Fc gamma receptor IIa) This gene encodes one member of a family of immunoglobulin Fc receptor genes found on the surface of many immune response cells. The protein encoded by this gene is a cell surface receptor found on phagocytic cells such as macrophages and neutrophils, and is involved in the process of phagocytosis and clearing of immune complexes. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -17 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.67).
BP6
Variant 1-161506437-C-T is Benign according to our data. Variant chr1-161506437-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 714935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-161506437-C-T is described in Lovd as [Likely_benign].
BP7
Synonymous conserved (PhyloP=0.476 with no splicing effect.
BS2
High Homozygotes in GnomAdExome4 at 2 AR gene
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00202 AC: 308AN: 152196Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.00183 AC: 460AN: 251482Hom.: 0 AF XY: 0.00185 AC XY: 252AN XY: 135918
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GnomAD4 exome AF: 0.00254 AC: 3717AN: 1461884Hom.: 2 Cov.: 32 AF XY: 0.00258 AC XY: 1876AN XY: 727244
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GnomAD4 genome AF: 0.00202 AC: 308AN: 152314Hom.: 1 Cov.: 32 AF XY: 0.00197 AC XY: 147AN XY: 74482
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:5
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2024 | FCGR2A: BP4, BP7 - |
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jul 06, 2018 | - - |
Likely benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at