19-16890234-G-T
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Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_003950.4(F2RL3):c.771G>T(p.Leu257=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000628 in 1,574,578 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0036 ( 1 hom., cov: 33)
Exomes 𝑓: 0.00031 ( 1 hom. )
Consequence
F2RL3
NM_003950.4 synonymous
NM_003950.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.834
Genes affected
F2RL3 (HGNC:3540): (F2R like thrombin or trypsin receptor 3) This gene encodes a member of the protease-activated receptor subfamily, part of the G-protein coupled receptor 1 family of proteins. The encoded receptor is proteolytically processed to reveal an extracellular N-terminal tethered ligand that binds to and activates the receptor. This receptor plays a role in blood coagulation, inflammation and response to pain. Hypomethylation at this gene may be associated with lung cancer in human patients. [provided by RefSeq, Sep 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -7 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BP6
Variant 19-16890234-G-T is Benign according to our data. Variant chr19-16890234-G-T is described in ClinVar as [Benign]. Clinvar id is 714781.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.834 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
F2RL3 | NM_003950.4 | c.771G>T | p.Leu257= | synonymous_variant | 2/2 | ENST00000248076.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
F2RL3 | ENST00000248076.4 | c.771G>T | p.Leu257= | synonymous_variant | 2/2 | 1 | NM_003950.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00359 AC: 546AN: 152220Hom.: 1 Cov.: 33
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GnomAD3 exomes AF: 0.000929 AC: 176AN: 189438Hom.: 0 AF XY: 0.000712 AC XY: 74AN XY: 104000
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GnomAD4 exome AF: 0.000310 AC: 441AN: 1422240Hom.: 1 Cov.: 33 AF XY: 0.000273 AC XY: 193AN XY: 705978
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GnomAD4 genome AF: 0.00360 AC: 548AN: 152338Hom.: 1 Cov.: 33 AF XY: 0.00344 AC XY: 256AN XY: 74498
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | May 21, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at