5-76733023-C-T
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001992.5(F2R):c.798C>T(p.Tyr266=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000223 in 1,614,076 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000053 ( 1 hom., cov: 32)
Exomes 𝑓: 0.000019 ( 0 hom. )
Consequence
F2R
NM_001992.5 synonymous
NM_001992.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.539
Genes affected
F2R (HGNC:3537): (coagulation factor II thrombin receptor) Coagulation factor II receptor is a 7-transmembrane receptor involved in the regulation of thrombotic response. Proteolytic cleavage leads to the activation of the receptor. F2R is a G-protein coupled receptor family member. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.75).
BP6
Variant 5-76733023-C-T is Benign according to our data. Variant chr5-76733023-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 752650.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.539 with no splicing effect.
BS2
High AC in GnomAd4 at 8 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
F2R | NM_001992.5 | c.798C>T | p.Tyr266= | synonymous_variant | 2/2 | ENST00000319211.5 | |
F2R | NM_001311313.2 | c.435C>T | p.Tyr145= | synonymous_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
F2R | ENST00000319211.5 | c.798C>T | p.Tyr266= | synonymous_variant | 2/2 | 1 | NM_001992.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152196Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251312Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135826
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GnomAD4 exome AF: 0.0000192 AC: 28AN: 1461880Hom.: 0 Cov.: 32 AF XY: 0.0000179 AC XY: 13AN XY: 727244
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GnomAD4 genome AF: 0.0000526 AC: 8AN: 152196Hom.: 1 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74352
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jun 13, 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