rs7988959
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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.*3433T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.23 in 152,156 control chromosomes in the GnomAD database, including 4,433 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 ( 4433 hom., cov: 32)
Exomes 𝑓: 0.22 ( 0 hom. )
Consequence
FARP1
NM_005766.4 3_prime_UTR
NM_005766.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.89
Genes affected
STK24 (HGNC:11403): (serine/threonine kinase 24) This gene encodes a serine/threonine protein kinase that functions upstream of mitogen-activated protein kinase (MAPK) signaling. The encoded protein is cleaved into two chains by caspases; the N-terminal fragment (MST3/N) translocates to the nucleus and promotes programmed cells death. There is a pseudogene for this gene on chromosome X. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2013]
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=-0.9).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.294 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STK24 | NM_001032296.4 | c.*1423A>G | 3_prime_UTR_variant | 11/11 | ENST00000539966.6 | ||
FARP1 | NM_005766.4 | c.*3433T>C | 3_prime_UTR_variant | 27/27 | ENST00000319562.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FARP1 | ENST00000319562.11 | c.*3433T>C | 3_prime_UTR_variant | 27/27 | 1 | NM_005766.4 | P1 | ||
STK24 | ENST00000539966.6 | c.*1423A>G | 3_prime_UTR_variant | 11/11 | 1 | NM_001032296.4 | P1 | ||
STK24 | ENST00000376554.8 | c.*1423A>G | 3_prime_UTR_variant | 5/5 | 5 | ||||
STK24 | ENST00000397517.6 | c.*1423A>G | 3_prime_UTR_variant | 10/10 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.230 AC: 34909AN: 152006Hom.: 4431 Cov.: 32
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GnomAD4 exome AF: 0.219 AC: 7AN: 32Hom.: 0 Cov.: 0 AF XY: 0.182 AC XY: 4AN XY: 22
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GnomAD4 genome ? AF: 0.230 AC: 34917AN: 152124Hom.: 4433 Cov.: 32 AF XY: 0.225 AC XY: 16758AN XY: 74358
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ClinVar
Not reported inComputational scores
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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