rs2227831
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_001992.5(F2R):c.89-4645A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0261 in 152,126 control chromosomes in the GnomAD database, including 57 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.026 ( 57 hom., cov: 32)
Consequence
F2R
NM_001992.5 intron
NM_001992.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.462
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0261 (3974/152126) while in subpopulation NFE AF= 0.039 (2652/67998). AF 95% confidence interval is 0.0378. There are 57 homozygotes in gnomad4. There are 1913 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd4 at 3974 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
F2R | NM_001992.5 | c.89-4645A>G | intron_variant | ENST00000319211.5 | |||
F2R | NM_001311313.2 | c.-397-1043A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
F2R | ENST00000319211.5 | c.89-4645A>G | intron_variant | 1 | NM_001992.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0261 AC: 3971AN: 152016Hom.: 57 Cov.: 32
GnomAD3 genomes
?
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152016
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0261 AC: 3974AN: 152126Hom.: 57 Cov.: 32 AF XY: 0.0257 AC XY: 1913AN XY: 74368
GnomAD4 genome
?
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3974
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152126
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32
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1913
AN XY:
74368
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13
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at