rs12261
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_005766.4(FARP1):āc.3114T>Cā(p.Ser1038Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.565 in 1,612,630 control chromosomes in the GnomAD database, including 259,699 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: š 0.54 ( 22512 hom., cov: 33)
Exomes š: 0.57 ( 237187 hom. )
Consequence
FARP1
NM_005766.4 synonymous
NM_005766.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.127
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]
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.61).
BP7
Synonymous conserved (PhyloP=0.127 with no splicing effect.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.572 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FARP1 | NM_005766.4 | c.3114T>C | p.Ser1038Ser | synonymous_variant | 27/27 | ENST00000319562.11 | NP_005757.1 | |
STK24 | NM_001032296.4 | c.*4880A>G | 3_prime_UTR_variant | 11/11 | ENST00000539966.6 | NP_001027467.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FARP1 | ENST00000319562.11 | c.3114T>C | p.Ser1038Ser | synonymous_variant | 27/27 | 1 | NM_005766.4 | ENSP00000322926.6 | ||
FARP1 | ENST00000595437.5 | c.3207T>C | p.Ser1069Ser | synonymous_variant | 28/28 | 1 | ENSP00000471242.1 | |||
STK24 | ENST00000539966.6 | c.*4880A>G | 3_prime_UTR_variant | 11/11 | 1 | NM_001032296.4 | ENSP00000442539.2 | |||
FARP1 | ENST00000627049.2 | c.3207T>C | p.Ser1069Ser | synonymous_variant | 28/28 | 5 | ENSP00000486285.1 |
Frequencies
GnomAD3 genomes AF: 0.542 AC: 82330AN: 151980Hom.: 22495 Cov.: 33
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GnomAD3 exomes AF: 0.538 AC: 135237AN: 251400Hom.: 37178 AF XY: 0.540 AC XY: 73349AN XY: 135868
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GnomAD4 exome AF: 0.567 AC: 828766AN: 1460532Hom.: 237187 Cov.: 39 AF XY: 0.565 AC XY: 410292AN XY: 726696
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GnomAD4 genome AF: 0.542 AC: 82381AN: 152098Hom.: 22512 Cov.: 33 AF XY: 0.542 AC XY: 40331AN XY: 74352
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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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at