rs11681497
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_014808.4(FARP2):c.331+77A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 1,091,714 control chromosomes in the GnomAD database, including 6,080 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 0.10 ( 846 hom., cov: 33)
Exomes 𝑓: 0.10 ( 5234 hom. )
Consequence
FARP2
NM_014808.4 intron
NM_014808.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.296
Genes affected
FARP2 (HGNC:16460): (FERM, ARH/RhoGEF and pleckstrin domain protein 2) Enables guanyl-nucleotide exchange factor activity. Acts upstream of or within Rac protein signal transduction and neuron remodeling. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.94).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.106 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FARP2 | NM_014808.4 | c.331+77A>G | intron_variant | ENST00000264042.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FARP2 | ENST00000264042.8 | c.331+77A>G | intron_variant | 1 | NM_014808.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.100 AC: 15285AN: 152106Hom.: 844 Cov.: 33
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GnomAD4 exome AF: 0.104 AC: 97436AN: 939490Hom.: 5234 AF XY: 0.103 AC XY: 50354AN XY: 487858
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GnomAD4 genome ? AF: 0.101 AC: 15299AN: 152224Hom.: 846 Cov.: 33 AF XY: 0.0975 AC XY: 7260AN XY: 74426
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ClinVar
Not reported inComputational scores
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Name
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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