rs584800
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_005766.4(FARP1):c.759+19C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 1,611,108 control chromosomes in the GnomAD database, including 31,271 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 0.23 ( 4424 hom., cov: 32)
Exomes 𝑓: 0.19 ( 26847 hom. )
Consequence
FARP1
NM_005766.4 intron
NM_005766.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.399
Genes affected
FARP1 (HGNC:3591): (FERM, ARH/RhoGEF and pleckstrin domain protein 1) This gene encodes a protein containing a FERM (4.2, exrin, radixin, moesin) domain, a Dbl homology domain, and two pleckstrin homology domains. These domains are found in guanine nucleotide exchange factors and proteins that link the cytoskeleton to the cell membrane. The encoded protein functions in neurons to promote dendritic growth. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2013]
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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=-0.82).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FARP1 | NM_005766.4 | c.759+19C>T | intron_variant | ENST00000319562.11 | |||
FARP1 | NM_001286839.2 | c.759+19C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FARP1 | ENST00000319562.11 | c.759+19C>T | intron_variant | 1 | NM_005766.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.229 AC: 34878AN: 152024Hom.: 4409 Cov.: 32
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GnomAD3 exomes AF: 0.205 AC: 51178AN: 249376Hom.: 5644 AF XY: 0.201 AC XY: 27144AN XY: 134896
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GnomAD4 exome AF: 0.187 AC: 273522AN: 1458966Hom.: 26847 Cov.: 31 AF XY: 0.188 AC XY: 136242AN XY: 725610
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GnomAD4 genome ? AF: 0.230 AC: 34930AN: 152142Hom.: 4424 Cov.: 32 AF XY: 0.231 AC XY: 17152AN XY: 74376
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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